Anime-Manga Differences

This page lists the differences that occurred during the transition from manga to anime.

Censorship
These are changes made in the anime for the young audience where originally in the source material, the content is unsuitable. Note that many of these censored scenes are generally still included in the uncut DVD releases (with some exceptions) and that most are aimed at the original broadcast release.

Part I

 * In the manga, when Mizuki throws multiple kunai at Iruka, Iruka pulls a kunai out of his chest. In the anime, none of the kunai hit his chest and he pulls a kunai out of his right leg instead.
 * In the manga, Ebisu fixes his glasses with his middle finger. In the anime, he also uses his index finger.
 * In the manga, during the bell test at the Third Training Ground, Sasuke unleashes a barrage of shuriken and kunai that directly impale Kakashi in the face which causes blood to spray out from a front angle. In the anime, he is pushed aside quickly and only the scene of him viewed from behind is left.
 * During the bell test, Kakashi casts a genjutsu spell on Sakura, showing her a gravely injured Sasuke. In the manga, "Sasuke" has a missing left arm, a twisted left leg and numerous kunai impaling his body. In the anime, he has his arm and leg intact and has only a few kunai impaling his body. As a result of the genjutsu, Sakura is rendered unconscious on the ground. The manga played up the more intense and comical spaz attack by showing an unconscious Sakura with wide blank eyes and seizure-like foam at the mouth.
 * In the manga, after the Demon Brothers capture and seemingly kill Kakashi, a silhouette of different body parts being shred apart is shown. In the anime, much of the blood and gore is removed.
 * In the manga, when Kakashi is describing the role of hunter-nin a severed hand that is impaled with a knife is shown. In the anime, this is removed.
 * In the manga, in the flashback scene where Kaiza is crucified and then executed, his arms have also been chopped off. In the anime, they are instead only badly broken and burned.
 * In the manga, when Kakashi unintentionally killed Haku with his Lightning Cutter, his hand pierced his body, with his hand visibly coming out of Haku's back. However, in the anime, Kakashi's hand only pierced the front of Haku's chest.
 * In the manga, when Gatō arrives and sees Haku's corpse, he is seen kicking him across the face as payback for when Haku nearly broke his arm. However in the anime, the kick to his face is not seen, and only Naruto's look of shock is seen instead.
 * In the manga, Zabuza stabs Gatō in the chest and then decapitates Gatō to kill him, while in the anime, Zabuza stabs Gatō in the chest and then instead slashes him multiple times across the chest, which results in Gatō falling off the bridge to his death.
 * In the manga, when Anko Mitarashi threw a kunai at Naruto and cut his cheek, she licks the blood directly from Naruto's cheek. In the anime, she only touches the blood from his cheek with her fingers.
 * In the manga, during the second phase of the Chūnin Exams, Team 8 gets their second scroll by luring a fellow Konoha team into a trap filled with Poisonous Leeches. In the anime, it was changed to a team from Amegakure.
 * In the manga, when Anko views the tape showing the arrival of the Three Sand Siblings at the tower, there is blood splatter and two sets of feet on the ground, heavily implying that Gaara killed another team of Genin to sate his bloodlust due to Kankurō and Temari convincing him to spare Team 8. The anime removed this.
 * In the manga, when Gaara is about to kill Baiu and Midare, Temari says goodbye to them and also waves goodbye with a big smile on her face. The anime removed this.
 * In the manga, during the preliminary rounds of the Chūnin Exams, Zaku Abumi's right arm is blown off when Shino Aburame uses his bugs to block Zaku's air tubes. In the anime, both of Zaku's arms remain attached to his body, only the skin on his arms break.
 * In the manga, when Gaara attacks and kills Dosu using the power of Shukaku, the attack bifurcated Dosu, which is seen when the dust cloud Gaara created had cleared up. In the anime only Dosu's injured arm was shown after the fatal attack and unlike the manga Gaara is also seen using this attack directly.
 * In the manga, when the corpse of Hayate Gekkō is shown, there is a great amount of blood and even carrion birds picking at his corpse. However, in the anime, much of the blood and the carrion birds are removed.
 * The design of the Hyūga Main Family's Juinjutsu is different in the manga and anime. In the manga, it was a variation of a manji, a Buddhist symbol, but due to its similarity in appearance to the swastika, it was altered into an X in the anime to avoid confusion.
 * In the manga, when Gaara brutally murdered Shiba and Midori (which was not shown in detail), the hallway was completely splattered with their blood and body parts, to which Gaara even stepped on. The anime significantly reduced this by showing their murders in detail, but instead they were completely crushed within Gaara's sand, blood and bodies buried within it. Midori's attempt to escape before being dragged back in was exclusive to the anime as well.
 * In the manga, when Kakashi defends Sakura against two Oto-nin, he impales them in the head with kunai. In the anime, he slashes them across the chest with kunai instead.
 * In the manga, after Asuma rescues Shikamaru from a group of Oto-nin, he slashes them and punches using his trench knives, leaving their bloody corpses to the floor, he then flicks his cigarette into a pool of their blood. In the anime, the brutal assault was censored with Asuma only punching them with the trench knives and never slashing them or smoking a cigarette.
 * In the manga, when Hiruzen Sarutobi raids Orochimaru's lair, there are several corpses strung along the walls. In the anime, these corpses are replaced with shelves containing jars filled with remains and various organs.
 * In the manga, when Gaara presses Sakura up against a tree, blood trickles out of her mouth. In the anime, this is removed.
 * In the manga, when a young Gaara attempted to cut himself in a flashback, he aimed for his wrist, at the vein. In the anime, he aimed at the back of his hand instead.
 * As Naruto walks through the festival city, he stops by a mask shop and purchases a mask. Various masks in the background represent past Japanese manga, anime and tv series "in-jokes" included by Kishimoto. These include masks of Kamen Rider and Chiaotzu from the Dragon Ball series. The anime changed many of these to generic masks.
 * In the manga, when Kabuto goes for blood to summon snakes, he retrieves it from the wound on his wrist. In the anime, he retrieves the blood from a wound on his palm instead.
 * A minor edit concerning the location of the small shinobi animals, Gamatatsu, Gamakichi and Tonton are all in the thick of the action when the giant snakes begin to attack.
 * Related to the previous entry, Tonton was among the injured fallen in the manga. In the anime, the three shinobi animals moved away to safety early on.
 * In the manga, when Naruto prevents Kabuto Yakushi from attacking Tsunade, Kabuto's kunai directly impales Naruto's hand. In the anime, it gets caught between Naruto's fingers instead.
 * In the manga, especially in Part I, Naruto and Kiba "flip the bird" several times, in the English adaptation of the manga and in the anime they only close their fist and look angry.
 * Kidōmaru did his best to take down Neji, this was especially apparent in the original manga, where his first arrow ripped a massive hole through Neji's shoulder. The anime greatly reduced the size of the hole. While this may serve as a content edit, it also made it more feasible for Neji to live through such an attack.
 * In the manga, when Shikamaru Nara gets caught in Tayuya's genjutsu, he sees his skin and flesh melt off of his bones. In the anime, he sees his entire arm melt away including the bones.
 * In the manga, after Raidō Namiashi and Genma Shiranui are defeated by the Sound Four, Raidō has three shuriken in his back and Genma has two kunai in his chest with his left palm facing up. In the anime, Raidō has two shuriken and a single kunai in his back and Genma has a single kunai in his chest with his left palm facing down.
 * In the manga, while Kimimaro is fighting Gaara, Kimimaro's bones came out of his fingertips by dividing his skin on his fingertips. In the anime, his bones just emerged from his fingertips through holes that close afterwards.
 * Kimimaro's encasement within Gaara's sand and his subsequent crushing are accompanied by a significant amount of more blood in the manga.
 * When Sasuke pierces through Naruto's shoulder with Chidori, we see his arm and hand with no obstruction. In the anime, they lessened the violent nature of the strike by whiting out the arm and hand with Chidori's electrical light.

Part II

 * When Team Kakashi decided to rest at a hot springs inn, the women bathing had towels and other objects added to block their nudity.
 * When Sai switches allegiances, he had subdued Kabuto in an alternate fashion in the anime. This was probably changed because Kabuto's hands were left free in the manga, making escape seem possible.
 * In the manga, Konohamaru Sarutobi has a sexy technique that depicts Sasuke and Sai in a sexual position. In the English version of the manga only a silhouette of the two is visible, and in the anime this is taken out entirely.
 * In the manga, Shikamaru is briefly seen smoking after Asuma's death. However, in the English adaptation of the manga and in the anime, he doesn't smoke; he only carries Asuma's lighter around with him; although at a certain moment, after he's done visiting Asuma's grave, he leaves a lit cigarette.
 * In the manga when Guren is making his escape from the northern hideout, he brutally kills a number of guards and there is a significant amount of blood. In the anime the blood is removed completely.
 * In the manga, when Nagato gets exhausted from overusing the Chibaku Tensei he coughed up a lot of blood. In the anime, however, this was changed to a trickle of saliva.
 * In the manga, when "Kisame" was decapitated, the head landed in front of Sabu. In the anime, this was omitted.
 * In the manga, after Danzō had badmouthed Itachi in the clutches of Sasuke's Susanoo, the latter crushed him. The amount of blood was heavily reduced in the anime, and the blood spattering on Sasuke's face was removed.
 * Interestingly, when Furui was impaled by the Eight-Tails, it was more censored than when it occurred in the anime as he was seen as a silhouette in the manga.
 * When Kisame slaughtered the Cypher Division in the anime, the action is censored.
 * When Armadiko's gender is revealed due to the Island Turtle being flipped upside down, its genitals are clearly shown in the manga. In the anime, the genitals are removed entirely.
 * In the manga, when Kankurō uses his Black Secret Technique — Machine Triple Shot, blood is seen draining from the Kuroari with Karasu in it. In the anime episode, the blood is omitted.
 * In the manga, when Gari blows up Tajiki, his blood spatters on his comrade. In the anime, the blood is removed.
 * Shippūden episode 272 was censored somewhat:
 * The gash Mifune sustained to his head was not shown despite him bleeding. In the manga, the gash was clearly visible.
 * When Mifune used Iai Beheading to cut open Ibuse's head, indications of the head being cleaved open are visible. In the anime, however, smoke covered this entirely.
 * When the Demonic Statue of the Outer Path rushes towards Chōji and Chōza, several shinobi are crushed by its feet or blown away from the shock wave. In the anime, this was omitted.
 * In Shippūden episode 278 when Sakura Haruno pulverised the transformed White Zetsu Army clone, no blood was seen coming from its mouth, whereas in the manga, there was blood.
 * In the manga, when the Second Mizukage's clone attacks the shinobi of the Fourth Division, he critically slashes one with his axe-like weapon. In the anime, he simply uses taijutsu.
 * In the manga omake tie-in, prior to Lee crashing in the girls public bath side, they were getting dressed. In the adapted anime episode, this was removed.
 * In the manga, when Madara reveals the status of the Kage, A had a large puddle of blood coming from his mouth. In the anime, this was removed, as well as a reduction of blood from the other Kage.
 * In the manga, when Obito states his dislike for Tobi the Zetsu clone, the latter "flips the bird" at him. In the anime, Tobi, nicknamed Guruguru by Obito, gives Obito a thumbs down.
 * Despite Obito's graphic massacre and massive amount of blood in the manga, there was very little censoring of it in the anime. In the original Japanese TV broadcast, the climactic battle was censored, with several seconds of gore cut and some sound effects muted. The footage was restored in the DVD release. However, in the following episode, the blood covering Obito is coloured black until he returns to Mountains' Graveyard.
 * In the manga, when the Ten-Tails took on its second form, a shinobi was seen coughing up blood after being injured by the impact of the transformation. This was only heard in the anime. In the same episode, Neji being impaled by the Ten-Tails wood branches in front of Naruto and Hinata was not shown in a close-up view.
 * In the manga, within his subconscious, Obito was being torn apart from the Ten-Tails' influence. The moment where his head was tearing apart was censored in the anime, only a glimpse of it is shown.
 * In the manga, Chōmei was absent when Madara was planning to go after the tailed beasts. In the anime, it was present alongside the other tailed beasts.
 * In the manga, Naruto's shadow clone hit by Kaguya's All-Killing Ash Bones screamed while crumbling to ashes. In the anime, the clone remained silent.
 * In the manga, when Naruto calls to Kurama joyfully, its irritation to Naruto's attitude is further shown by "flipping-off" Naruto. In the anime, Kurama merely exerts a clenched fist.

New Era

 * In the manga, Log is briefly seen smoking when having a conversation with Orochimaru. However, in the anime, he instead flicks his lighter.

Plot and Content Changes
These are changes that differ from the source material, usually made to accommodate for filler arcs or expanding material.

Part I

 * In the anime, Sasuke, Sakura and their classmates from Team 8 and 10 are introduced at the beginning of the story. In the manga Sasuke and Sakura first appeared in the third chapter, the other six were introduced at the beginning of the Chūnin Exam Arc.
 * In the manga, Naruto sneaks into the Hokage Residence to steal the Scroll of Seals and is caught by Hiruzen Sarutobi, but escapes by using Sexy Technique. In the anime, Hiruzen simply sends out the ninja after Naruto, and is exposed to the Sexy Technique when he refuses to accept Naruto's ninja registration photo.
 * In the manga, Iruka discards Mizuki's shuriken after he pulls it out of his back, but in the anime he throws it back at Mizuki.
 * In the manga, after Team 7 is formed, Sasuke is seen eating outside of a window with Naruto inside preparing an attack. In the anime, Sasuke is seen eating inside the window instead and Naruto attacks from outside.
 * In the manga, before battling Zabuza for the first time, Naruto throws two shuriken into the bushes, one of them nearly hitting a snow white rabbit. In anime, this was two kunai instead.
 * In the manga, Zabuza Momochi kills Kumade Toriichi with a tantō. In the anime, he uses a kunai.
 * In the manga, when Kakashi tells Zabuza that his future is death, he only has his Sharingan eye open. In the anime, both of his eyes are open.
 * In the manga after Kakashi's first encounter with Zabuza, Team 7 attempts to look at his face while he is sleeping. In the anime, this event is simply skipped.
 * In the manga, Chidori surrounds the user's hand in lightning. In the anime, it creates lightning in the palm of the user's hand.
 * In the manga, when Anko Mitarashi fights Orochimaru, she used daggers. However, in the anime, she used senbon.
 * When Shikamaru, Ino and Chōji appear after Neji has spotted them, Shikamaru is to the left and Chōji to the right of Ino but after Neji starts to walk off, they change places.
 * In the manga, Tenten and Temari's fight was never shown, due to Sakura and Ino's conversation occurring during their fight. However in the anime, Tenten and Temari's match was shown due to Sakura and Ino's conversation occurring before Tenten and Temari's match.
 * In the manga, Kin Tsuchi uses no other techniques besides utilising senbon with bells in her match with Shikamaru. In the anime, she uses her bells to activate the Bell Ring Genjutsu.
 * In the manga Ebisu explains to Naruto about his lack of chakra control while still at Konoha Hospital before Kakashi had left. In the anime, he explains it while the two are having lunch at Ramen Ichiraku after Naruto fails a challenge proposed by Ebisu.
 * In the manga, Jiraiya starts Naruto's training at the Konoha Hot Springs. In the anime, he tries to escape from training by attempting to elude him through a series of antics, eventually he trains him nearby a river.
 * In the anime, Jiraya's conversation with Ebisu takes place before Dosu is killed by Gaara instead of after. Additionally, the anime moved the scene of Baki and Kabuto's conversation to take place immediately after Dosu's death instead of having Jiraiya's conversation in between both of these scenes.
 * In the manga, when Jiraiya has Naruto drain his normal chakra during the Summoning Technique training, he has Naruto continue to use the Water Surface Walking Practice. In the anime, Naruto instead uses the Shadow Clone Technique to create a large amount of Shadow Clones to face in a battle royale.
 * In the manga, Hiashi Hyūga tells Neji the details behind his father's death himself. In the anime, he hands him a scroll written by his father.
 * In the manga, after a disguised Kabuto Yakushi finishes healing Hinata, he knocks Kiba Inuzuka and his dog Akamaru unconscious during Naruto and Neji's fight. In the anime, he knocks them out during Sasuke's fight with Gaara, just as Akamaru recognises Kabuto's scent. However, when this scene is shown again in flashback in Naruto: Shippūden, it's depicted like in the manga.
 * In the manga, Sasuke and Kakashi arrive to the finals shortly after Shikamaru's match had ended. In the anime, the Third Hokage instead allows for another extension for Sasuke to arrive and he and Kakashi arrive just as Genma is about to cancel the match after the waiting time had expired.
 * In the manga, the Kusanagi looks more like a standard katana, while in the anime it is a double-edged jian.
 * During the Third Hokage's fight with Orochimaru he rams Monkey King: Enma, who has transformed into an adamantine staff, into the Sword of Kusanagi, and his Enma is shown partially reversing the transformation. In the anime, this is removed.
 * In the manga, immediately after ramming his adamantine staff into the Sword of Kusanagi, Hiruzen Sarutobi places explosive tags on the left leg of Hashirama Senju and the right leg of Tobirama Senju, they are later shown healing while standing. In the anime, the tags are placed on the left leg of Hashirama and the right arm of Tobirama, they are shown healing while lying face down.
 * In the manga, Hashirama Senju uses the Bringer-of-Darkness Technique. In the anime, Tobirama Senju performs it.
 * In the manga, Shikaku Nara, Inoichi Yamanaka, and Chōza Akimichi first appeared during the Konoha Crush storyline as part of the counteroffensive alongside other family members of the Konoha 11. In the anime, they were originally introduced earlier during the Konoha Festival in the Chūnin Exams arc.
 * In the manga, when Naruto and Gamabunta do the Combination Transformation they transform into a giant fox with a single tail. In the anime, they transform into Kurama.
 * In the manga, when Jiraiya uses Rasengan on Gantetsu, he also steals his wallet, while in the anime, he is given it out of respect.
 * During Jiraiya and Naruto's search for Tsunade, Jiraiya enters a gambling parlour. While Naruto mills around he finds a coin on the ground. Wondering how the slot machine works, he decides to insert his coin. We then see Naruto has amazing luck, as he wins back an large amount of money. In the anime, this was changed to have Naruto win a lot of money in a lottery instead.
 * In the manga, after the group returns to the village with Tsunade and encounter Shikamaru and his father Shikaku, Jiraiya smacked Naruto on the head after hearing Naruto state to Shikamaru he'll show him his new move explaining that a shinobi shouldn't show off their techniques. This was skipped in the anime due to the fact that Jiraiya was left behind in the hot springs they visited in the previous episode.
 * In the manga, Shikamaru was promoted to a chūnin at some point before Naruto and Jiraiya returned from their journey of bringing Tsunade back to the village. In the anime, due to filler episodes taking place first, including the Land of Tea Escort Mission, this was pushed back to after Tsunade had become the Hokage and she was the one who personally informed Shikamaru of his promotion.
 * In the manga, Lee and Guy's conversation regarding that Lee should go through the risky surgery so Lee could fulfil his dream takes place on the same night Sasuke fought against the Sound Four. In the anime, this took place after Tsunade returned to the village at the end of the Search for Tsunade arc.
 * In the anime, Tsunade's talk with Lee about why he wants to go through with the surgery before mentioning that the surgery was to take place that afternoon occurred at the beginning of the Sasuke Recovery Mission arc on the same day that Naruto and Sasuke fought. In the manga, this scene along with the surgery takes place on the following day shortly after the Sasuke Retrieval Team left the village.
 * In the manga, Sakura takes Naruto with her to a park bench just after Sasuke left following their battle to tell him about Sasuke's curse mark. In the anime, she instead accepts a small dinner date with Naruto at Ramen Ichiraku in the evening to talk about it there which occurred during Sasuke's battle with the Sound Four.
 * In the manga, Neji was recruited into the Sasuke Retrieval Team after Lee heard their conversation and recommended him. In the anime, the team instead encountered both him and Lee on their way out of the village discussing the success of Lee's operation that took place the day before.
 * In the manga, Kiba is forced to save Akamaru from an Explosive Tag when Akamaru accidentally tripped after setting it. In the anime, it is due to Sakon using wire to bind Akamaru to prevent him from escaping the blast.
 * In the manga, when Sakon and Ukon are torn apart and regenerate, the dark tissue leaks out of their body and forms new arms and legs. In the anime, the arms and legs are formed out of their organs.
 * After bringing Naruto back from the Valley of the End, Kakashi goes to the Memorial Stone to talk with Obito. This brief scene was taken out to be used in a later episode. This chapter and the next were greatly rearranged and split up over the course of 80+ episodes of filler. This filler was used to allow the manga to get further ahead.
 * In the anime, when Neji suggests to Hinata that she go see Naruto off, he is in the middle of sparring with her. In the manga, it is in the middle of his sparring session with Hiashi, and the conversation is much longer, including an appearance from Kiba and Shino. The scene of Neji's training session with Hiashi and Kiba and Shino's appearance was instead used earlier in the anime at the beginning of the Mizuki Tracking Mission.

Part II

 * In the manga, when Naruto returns from his training with Jiraiya, the person he first re-encounters is Kakashi. In the anime, he first meets Sakura and Konohamaru. Also, Naruto meets Shikamaru and Temari on the streets in the manga, while in the anime he meets them while inside Tsunade's office.
 * In the manga, Yurika told Tsunade herself about Gaara's kidnapping, while in the anime, she handed her the message to read it.
 * In the manga, Neji examines with his Byakugan inside the cave of the Land of River before Team Kakashi and Chiyo arrive. In the anime, however, Neji examines inside the cave after Team Kakashi and Chiyo arrive.
 * In the manga, Hiruko was a normal puppet, in the anime, he was a Human Puppet.
 * During the Kazekage Rescue Mission, an unknown Akatsuki member is present in various scenes during Shukaku's sealing. However, this member is replaced with Hidan in the anime.
 * In the manga, none of the puppets in Chiyo's Chikamatsu collection were destroyed, however in the anime, at least four were shown being heavily damaged.
 * In the manga, Kakashi explains Naruto's Multiple Shadow Clone Technique training method before teaching him about nature transformation, with Yamato being present for the latter. In the anime, he instead explains nature transformation first and Yamato arrives partway through the explanation.
 * In Shippūden episode 80, Asuma is shown buying flowers from the Yamanaka Flower Shop after the time skip. In the manga, he bought the flowers before the time skip.
 * During Naruto's training to add his wind nature to the Rasengan, Kakashi takes him to Ramen Ichiraku. In the manga, Ayame is away on a trip and Nishi and Matsu work as her replacements. In the anime, she has just returned from a trip and has converted the Ramen Bar into a Tsukemen bar.
 * In the manga, after Konohamaru performed the Sexy Girl on Girl Technique, Sakura punched him for using it. But in the anime, Moegi punched him instead.
 * In the manga, Shiba picked up Sasuke's scent while in the anime, it was Bisuke.
 * In the manga, Sasuke's first encounter with Itachi takes place while Jiraiya is infiltrating Amegakure, along with the later events of Hebi heading to Itachi's location.   In the anime, this instead takes place after Jiraiya's death.
 * In the manga, Naruto finds out about Jiraiya's death just before Sasuke is assigned to capture Killer B. In the anime, due to the Six-Tails Unleashed filler arc, this was pushed back to afterwards, where instead it is shown at the beginning of the Pain's Assault arc.
 * In the manga, Utakata, the jinchūriki of the Six-Tails, had already been captured by the time of Akatsuki and Taka's alliance, while in the anime he was captured afterwards.
 * In the manga, Tobi blocks Suigetsu's sword with his artificial right arm. In the anime, he blocks it with his left arm.
 * In the manga, when decoding Jiraiya's message, Shiho shows the correct way to write 'ta' and the way that Jiraiya did, and in the anime however, Shikamaru does this. In the anime, they also confirm it by comparing the 'ta' with a book containing Jiraiya's writing in it.
 * In the manga, Pain's Giant Rhino summon first appeared in during the invasion of Konoha. In the anime, he summoned it during the fight with Jiraiya.
 * In Shippūden episode 157, there are a few changes:
 * In the manga, when the assault on Konoha began, the Animal Path summoned one centipede that was killed by Sakura. In the anime, three centipedes were summoned, one that was killed by Sakura as in the manga, and later another that was killed by Shikamaru. The third one's fate however was unseen.
 * In the manga, after Kakashi saves him from Pain, Iruka informs Sakura that Akatsuki is invading the village. In the anime, Iruka informs Sakura of the attack but has no idea who is invading, which happened before his encounter with Pain.
 * In the manga, Ino's first thought about Katsuyu was that the slug was part of the enemy's attack during Pain's invasion. In the anime however, this incident happened earlier during the Three-Tails' Appearance, when four divisions of Katsuyu appeared in time to help the sealing team by giving them an extra supply of chakra. Ino and Hinata, who did not recognise Katsuyu, were initially alarmed until Sakura explained who Katsuyu was to them.
 * In the manga, Naruto teaches Konohamaru the Rasengan before the time-skip. In the anime, he teaches it after the time-skip.
 * In the manga, Human Path throws Animal Path away from the Rasenshuriken blast after grabbing hold of the back of her cloak collar. In the anime, he does it by the front of her cloak collar.
 * In the manga, Hinata charged straight at Deva Path. In the anime, she focused more on trying to free Naruto from his restraints than attacking Pain.
 * In the manga chapter #449 when Sasuke and his team are seen getting ready to head to Konoha, Suigetsu already had the Kubikiribōchō back and was wearing a robe. In the anime, he was seen coming back after retrieving the Kubikiribōchō and wearing his regular outfit.
 * In the manga, Tokuma Hyūga and Ranka are introduced after the Kage Summit. In the anime, they're introduced before.
 * In the manga, Mei Terumī strikes Ao with a straight punch. In the anime, she strikes him with an uppercut.
 * In the manga, Sasuke is the one to cut Danzō Shimura's arm off and slash into his torso. In the anime episode where the scene is extended, Garuda is the one that cuts Danzō's right arm off.
 * In the manga, an unknown shinobi interrupts the Fire Daimyō's appointment of Kakashi as Hokage with news of Tsunade waking up, while in the anime, Guy is the one to interrupt the meeting while an unknown shinobi is seen alongside Shizune.
 * In Shippūden episode 246, the fact that Kushina migrated to Konohagakure is played on very heavily. She even stated that she didn't hold much hope to be rescued when kidnapped by Kumo-nin because she was an "outsider". However, in the manga, this is not the case as she told Naruto that Konoha immediately sent out a search party to look for her.
 * In the manga, when Hiruzen is driving the Nine-Tailed Demon Fox out of Konohagakure, his team-mates Homura, Koharu and even Torifu are present with him. In the episode that covered this chapter however, the scene is changed entirely.
 * In the manga, when Kisame Hoshigaki attempted to escape his pursuers at the Falls of Truth by travelling inside of his Water Release: Water Shark Bullet Technique, he did so by swimming through the water. In the anime, both the shark and Kisame flew through the air instead.
 * In the manga, during Kisame's flashback, the Cypher Division is attacked as they're eating, and all are killed at once by Kisame. In the anime, Kisame detects the enemies and tries saving the Cypher Division, but ends up killing them one at the time.
 * In Shippūden episode 261, genin from Sunagakure such as Matsuri are present in the war despite the fact that they would most likely not be allowed to participate. They were also not seen in the manga.
 * In the manga, when Shin and the Sasori puppet clash, the puppet uses its flamethrower. In the anime, however, it doesn't.
 * In the manga, when Kitsuchi and Kurotsuchi unearthed the White Zetsu, the Fifth Division began their attack. In the anime, after the unearthing, the attack was cut and moved to a later episode. However, Hana Inuzuka and Karui's involvement remained cut.
 * In the manga, a shinobi mentions that Haku is a member of the Yuki clan. In the anime, there is no such passage, and Haku is only mentioned as an Ice Release user by Sakura.
 * When Pakura attacks the Alliance's shinobi with her Scorch Release, in the manga she attacks an Iwagakure and a Konohagakure shinobi. In the anime she confronts two Konohagakure shinobi with taijutsu initially and by the time she uses the technique, one of the Konoha shiniobi becomes an Iwagakure shinobi.
 * It was said by an unknown Iwagakure shinobi that Gari was the former captain of the Iwagakure's Explosion Corps. However, in the manga, he was said to be the former member of the given organisation.
 * In the manga, Suigetsu is shown freeing Jūgo when the chapter focuses on them. The anime expands that sequence, showing how Suigetsu escaped his cell. During that time in the manga, Suigetsu's clothes was also shown to be in a semi-liquid state. In the anime, however, only his body is still in this state.
 * In the manga, Asuma noticed the arrival of his students before they faced Kinkaku. In the anime, this was omitted altogether.
 * In the manga, the Yamanaka, Nara, and Akimichi Clan Memorial was depicted with inscriptions beneath the clan symbols. This is removed altogether in the anime.
 * In the anime, Kabuto withdrew his reincarnated soldiers from the battlefield for the process of the night. In the manga, there was no indication for this.
 * In Shippūden episode 296, there are a few errors:
 * Naruto attacked the first Zetsu disguised as F with a Rasengan, despite kicking him in the manga.
 * The first group of Zetsu being defeated by Naruto already changed back to their true form. In the manga, however, they still remained disguised as Allied Shinobi Forces.
 * In the manga, Toroi merely appears to summon larger shuriken from his scroll. In the anime, he withdrew regular-sized shuriken from his sleeves, and enlarged them.
 * In Shippūden episode 321, there are a few errors/changes:
 * Naruto attacked the two Zetsu disguised as Iwa-nin in the Logistical Support and Medical Division with his body, despite using his Spiralling Serial Spheres in the manga.
 * When Kakashi manages to slice through Fuguki's torso with the Kubikiribōchō, he just sliced him with the sword. In the manga, Kakashi applied a lightning chakra flow on the sword to increase its piercing..
 * An additional part of the Daimyō Protection Squad's fight against Black Zetsu is shown near the beginning before Madara is summoned, while in the manga it is not shown..
 * Pakura, Gari and Mangetsu are shown fighting the Third Division along with Fuguki before retreating into the forest after Fuguki is sealed, while in the manga they are not shown and only mentioned by Lee that only three remain..
 * In Shippūden episode 324, Naruto is shown recognising Utakata, and finds himself inside a mental plane where he converses with Utakata, where the two reminisce about Hotaru and their previous interactions. In the manga, the two had no prior interaction and therefore do not communicate.
 * In Shippūden episode 329, when the jinchūriki and the tailed beasts introduce themselves to Naruto, small dialogue changes were made, Isobu commenting on meeting Naruto before, and Utakata telling Naruto that he already knew his name. In the manga, neither had met Naruto before, and therefore both introduce themselves normally.
 * In Shippūden episode 331, the contents of the scroll Suigetsu finds at one of Orochimaru's hideouts is shown. In the manga, the scroll's contents were not revealed until much later. Also, in the manga, Karin's chains were linked to a wall, in the anime they weren't linked to any walls.
 * In Shippūden episode 363, Neji is seen behind Kakashi when the Allied Shinobi Forces arrive to the battlefield. In the manga, a Kumo shinobi is behind him and Neji isn't seen among them.
 * The following scenes from the manga were omitted or changed in the anime episode 364:
 * A Sunagakure shinobi from the Intelligence Division having an argument with a Kirigakure shinobi from the Sensor Division about evacuating the place or not shortly before the Ten-Tails' Tailed Beast Ball hits the Alliance's headquarter.
 * An elderly Kumogakure shinobi praising the Hyūga clan's prowess on the battlefield.
 * In the manga, Sakura Haruno was saved from the Ten-Tails's rampage by Kakashi Hatake. In the anime, however, Sakura protected herself instead of being saved by Kakashi.
 * The shinobi on the battlefield defending themselves against the Ten-Tails' Wood Release: Cutting Technique by using Earth Release and Fire Release.
 * Naruto throwing 3 Rasenshuriken towards the barrage of wooden spikes in the manga, slicing paths through the Cutting Technique and detonating midair. In the anime, Naruto throws 5, each one disabling one of the Ten-Tails' tails.
 * During Kakashi's flashback about a previous sparring with Obito, the latter failed to perform the Fire Release: Great Fireball Technique. In the anime, however, his usage of the technique succeeded.
 * In the manga, once Naruto handed everyone in the Shinobi Alliance Nine-Tail Chakra Cloaks, an unnamed member of the Akimichi clan didn't gain a Nine-Tails Chakra Cloak in the background. In Shippūden episode 365, he was not present, and was replaced with Chōji Akimichi who had gained a Nine-Tails Chakra Cloak from Naruto.
 * In Shippūden episode 375, once Obito sealed the Ten-Tails into himself, a shell encased around him and shattered once the jinchūriki transformation was complete. Originally in the manga, the transformation was unclear. In Shippūden episode 378, however, the transformation was the same as it was in the manga in Hinata's flashback.
 * In the manga, when Obito attempted to attack Naruto, Sasuke shielded the latter using the hand of his Susanoo. The hand was penetrated, while in the anime, the attack did not pierce through.
 * In the manga, when Madara activates the Infinite Tsukuyomi, Yamato is already under the genjutsu once Tobi releases him. When he is released in the anime, Yamato quickly gains consciousness, asking Hiruzen about what has taken place in the war, and only then gets caught in the genjutsu.
 * In Shippūden episode 476, there are several changes:
 * Naruto's vision of Neji Hyūga urging him to succeed in saving Sasuke did not occur in the manga.
 * While explaining his interpretation of the Hokage, Sasuke catching and crushing a floating leaf to allude to his detachment from the current Konohagakure is original to the anime.
 * In the manga, Hagoromo Ōtsutsuki recalled becoming a new form of Hokage as Sasuke's answer to his previous question. In the anime, this was omitted. However, he was later shown disappearing unlike in the manga.
 * In the manga, both Naruto and Sasuke recall some of their past conversations with Itachi.  In the anime, these scenes are either skipped entirely or shown at a different time of the conversation.
 * In the manga, several characters of the series are seen behind Naruto while he explained that he learned everything from the people of the past. In the anime, the characters aren't shown.
 * The fight between Naruto and Sasuke starts with clashing their arms against each other on top of Hashirama's statue. In the anime however, the two run down the statues and clash in the middle of the lake, all while their development over the course of the series is shown. Additionally, the following fighting sequences up until Naruto blocks Sasuke's Fire Release: Great Fireball Technique with a chakra arm are original to the anime.
 * The Great Fireball Technique mentioned above is depicted much stronger in the anime than in the manga, pushing against Naruto's defense with such power that the ground under his feet starts to crack.
 * When Naruto and Sasuke recall meeting in the past, the grown up Naruto is standing next to the younger Sasuke and vice versa. In the manga, this detail wasn't shown.
 * In the manga, Naruto recalls Jiraiya and Sasuke's earlier explanation during the fight. In the anime, these scenes aren't shown.
 * Sasuke's usage of Kirin only occurs in the anime.
 * In the anime, Naruto's recollection of Sasuke stating that top-class shinobi could understand each other when their fists meet is omitted.
 * In Shippūden episode 477, there are some changes:
 * In the manga, Naruto summons three shadow clones in his Tailed Beast Mode. In the anime, he summons four.
 * One of the clones mentioned above was defeated in the course of the ensuing battle, which was also expanded and shown in more detail than in the manga.
 * The sky in the manga was free of clouds, providing a full view of the ground below. The anime had full cloud cover, which the duo punched through, continuing their battle above the clouds.
 * In the anime, the natural energy collected by Naruto's clone was depicted to visibly float upwards while in the manga, it was invisible.
 * In the manga, Naruto begins merging his Tailed Beast Mode with those of his clones into a single avatar before receiving the natural energy. In the anime, he does it only afterwards.
 * The aftermath of the clash between Indra's Arrow and Naruto's Six Paths: Ultra-Big Ball Rasenshuriken is shown in more detail, notably the massive crater the blast carves as well as a full view of the cloud formation partially shown in the manga, which resembles a supercell.
 * In Shippuden episode 479, there are a few changes.
 * In the manga, the funeral that was held after the war was for Neji. In the anime, it was expanded to also include all the people who died in the war and the graves of Shikaku and Inoichi were also seen.
 * In the manga, Sasuke was only seen after the war being told by Kakashi that he is being pardoned and therefore would not have to be imprisoned. In the anime, Sasuke was first seen imprisoned in Konoha's jail, before Kakashi had him pardoned and released.
 * In the manga, Guy's condition due to the injury to his right leg was implied only in the series' epilogue. In the anime, it was confirmed when a medical ninja informs the remaining Team Guy that the damage is permanent.

New Era

 * In the manga, Sakura was taken care in Shizune's residence. However, in the anime, Sakura was taken care in the Konoha Hospital.
 * After Naruto blocks Shin's attacks with Tailed Beast Chakra Arms, Sarada and Chōchō mention that they know Naruto having the Nine-Tails inside his body, while in the manga, they don't mention this fact.
 * An error occurs when Shin tries to fend off Naruto's chakra arms' assault with his shuriken on the chain, despite the fact that the shuriken was already dismantled by Shin a moment earlier to launch an attack on Naruto.
 * In the manga, after meeting Sarada, Sasuke has a flashback of him discussing the possible treat greater than Kaguya with Naruto, Sakura and other Kage on the Five Kage Summit. In the anime, during this flashback, he discussed the matter only with Naruto instead. Later in the anime, the Summit on that matter is eventually shown, although it's set in the present time instead of the flashback and Sasuke doesn't show up on it.
 * In the manga, Sakura got warped away by Shin Uchiha's Space–Time Dōjutsu of his creature while standing next to Shin and his clone. In the anime, Sarada was supposed to be the one warped away, but Sakura pushed her out of the way and was teleported in her place.
 * In the manga, when Naruto notices Sarada's Sharingan, he mentions her having it aloud. In the anime, he hands her a mirror to look on it.
 * In the manga, during their final encounter, Shin was quickly defeated by Sasuke catching off guard and crushing him with Susanoo. In the anime, the fight was extended, having Sasuke defeat Shin with Sakura's aid, teleporting her close enough to cripple him in a single blow.
 * In the manga, Gaara was with Team Shinki and Kankurō in the Thunder Rail. However, in the anime, Gaara wasn't with the others and instead he watched them off.

Animation Changes
These are subtle changes made in the anime.

Part I

 * In the anime, Zabuza's flak jacket design was altered by adding metal with the Kirigakure village symbol on each shoulder.
 * In the manga, an unnamed Chūnin Exams proctor is shown with a tattoo on his head.  In the anime, he is removed completely.
 * In the manga, up until the second part of the Chūnin Exams, Neji's hair tie was higher up, right at the base of his head. In the anime, it was much lower.
 * In the manga, Orochimaru's summoning tattoo has alternating curves coming out of it. In the anime, these are removed. This is corrected in subsequent appearances, but instead adds another error where the lower part of the seal is incorrect.
 * In the manga, when Kabuto speaks with Baki after Gaara killed Dosu, he wears a sleeveless outfit. In the anime, he wears his usual attire. In Shippūden episode 307, Kabuto wears a sleeveless purple shirt and blue pants, including his Konoha forehead protector.
 * In the manga, when Kabuto killed an Anbu during Naruto's battle with Neji at the Chūnin Exams, he wears an Anbu uniform. In the anime, he wears his usual attire instead of an Anbu uniform.
 * In the manga, when a member of the Anbu was killed by Kabuto during the final Chūnin Exams, his face was shown. However, in the anime, his face wasn't shown when he was killed.
 * In the manga, Hiruzen's outfit bore the kanji for on the back. In the anime, it was changed to the kanji for . His outfit once again bore the kanji for Third Hokage upon his reanimation.
 * In the manga, when Kabuto speaks with Orochimaru after the Invasion of Konoha ended, he was wearing a sleeveless outfit. In the anime, however, he wears his usual attire, including his Oto forehead protector and fingerless gloves.
 * In the anime at the Valley of the End, Naruto stands near to the statue of Madara Uchiha and Sasuke is opposite him. After the scene changes from Sasuke activating his Sharingan, Sasuke is near the statue with Naruto opposite him.

Part II

 * In the manga, when Yamato suppresses the Naruto's four-tailed form with Hokage-Style Sixty-Year-Old Technique — Kakuan Entering Society with Bliss-Bringing Hands, there are ten pillars. In the anime, there are eleven.
 * In the manga, the triangle on Hidan's Jashin amulet points up.
 * In Shippūden episode 80, when the lower portion of Pain's face is shown, he does not have his two lip piercings.
 * In the manga, a young Gamabunta is shown to not have had a scar on his left eye when sitting next to Jiraiya. In the anime, he has a scar.
 * In Shippūden episode 143, when B turns into the Eight-Tails, his shin-guards and sandals fall off. This didn't occur in the scene in the manga or any other time he has transformed.
 * In the manga, the Preta Path of Pain has six piercings below its mouth. In the anime, it only has five.
 * In the anime, the Naraka Path's original body, while still alive, is shown outside, while in the manga, he was in the sewers.
 * In the anime, the Asura Path's original body, while still alive, is shown wearing a rice hat, while in the manga, his bare forehead and crown of the head are shown.
 * In the manga Kushina's hair is shown to fall down almost to her ankles. In the anime, Kushina's hair falls to her waist.
 * In the manga, several of the Uchiha clan members before the founding of Konohagakure are depicted with elaborate facial markings. In the anime, however, only one of the members retain his distinct facial markings.
 * In the manga, Nagato deflects the Amegakure and Root kunai on his right. In the anime, he deflects them from his left.
 * In Shippūden episode 187, when Naruto looks at Hokage Rock before leaving with Jiraiya, Tsunade's face is next to Minato's, even though it was not there when they left at the end of Part I in the manga. In fact, when Naruto returned to Konoha, he claimed that the only thing different about the village was that Tsunade's face was now engraved on the rock. This seems to be a mistake from the animators as it contradicts a major part of the story line.
 * In the manga, when Danzō first reveals a Sharingan, the eye looks unhealthy, having a dark sclerae. In the anime, the sclerae is white.
 * In the manga, Rōshi's headpiece is depicted as having a golden ring on the left side. In the anime, however, this ring was not present.
 * In the manga, Sasuke's Susanoo has six fingers. In the anime, it has five fingers.
 * In the manga, when Sasuke puts Danzō in a genjutsu, "Itachi" uses Amaterasu with his right eye, In the anime, "Itachi" casts it with his left eye.
 * In Shippūden episode 214, there are several errors:
 * Kakashi's Mangekyō Sharingan is inaccurately depicted as having a black background and red tomoe, similar to Sasuke Uchiha's, though this was fixed in Shippūden episode 215.
 * The teeth of Sasuke's final Susanoo form in the manga are depicted as jagged, but when animated they resemble normal teeth with elongated canines.
 * When Sasuke's complete Susanoo is seen for the first time in the manga it has what appears to be an orb in it's foremost right hand. In the anime however the entity is seen with a gourd of sorts in its secondary right hand with the orb being absent altogether.
 * In the manga when White Zetsu cancels his Substitute Technique the clone resembles a regular Zetsu clone. However in the anime, the clone has the venus flytrap like extensions which have never been seen on a typical clone.
 * In Shippūden episode 221, the robes from all reincarnated Akatsuki members are depicted with an incorrect colour scheme, black with red lining. In the manga, the robes are wine-coloured with tan lining, matching Kabuto's. The colour scheme was corrected in Shippūden episode 254.
 * In the manga, the object Kurama was bounded to as well as the chains and stakes that bound it while sealed within Kushina Uzumaki had more of a liquid appearance while in the anime, they appear to be more solid. This was changed in the subsequent episode into something that resembled lava.
 * In the manga and in the Shippūden episode 247, Sasuke appeared to have short spiky black as an infant, however, in the Shippūden episode 248, he appears to have bangs on both sides of his face and no fringe
 * In Shippūden episode 255, there are several errors:
 * In the manga when Kabuto returns to the Mountains' Graveyard, he has several appendages on the lower half of his snake-like body. In the anime, however, these are not present.
 * In that same scene, Zetsu's lower half is completely white. Also in the manga, he appears close behind Kabuto while in the anime he is on the same side as Tobi.
 * In Shippūden episode 256, Hiashi Hyūga is seen wearing a bandanna-styled forehead protector whereas in the manga, he wears it in the traditional manner. This may have been misconstrued due to the fact that the forehead protector is on a dark cloth and Hiashi has black hair, but in fact the forehead protector is tied in as similar manner to Neji's: with his hair covering the back of the cloth.
 * In the manga, when Tsunade, A and Ōnoki are seen standing side by side, Ōnoki is actually flying. However, in the anime, he is not.
 * In Shippūden episode 261, C who was present in the manga when deploying with the Sensor Division, is replaced with another shinobi.
 * In the manga, Shin wears a Konoha forehead protector when he was reincarnated by Kabuto. In the anime, he doesn't wear one.
 * In the manga, when Omoi used the Cloud-Style Crescent Moon Beheading technique, he slashed his sword to the right and the opponents repelled the attack. In the anime, however, Omoi slashed to the left and the opponents dodged the attack instead.
 * In the anime, part of the left side of Tobi's face can be seen through his mask's eyehole. While in the manga, Masashi Kishimoto has consistently kept that side of his face, except for his eye, completely shadowed.
 * In the anime, Shin's eyes are depicted as being black. However, when he was reincarnated — the only time his eyes are seen open in the manga — they are depicted as being light-coloured. Curiously in the anime when Shin is reincarnated his eyes are black in colour, however when Sasori uses Shin as a puppet, his eyes turn white as if his personality had been eliminated by Kabuto which was not the case.
 * In Shippūden episode 264, there are a few changes:
 * In the manga, when he was reincarnated by Kabuto, Torune was drooling. In the anime, blood was coming from his mouth.
 * The Suna-nin that speaks with the shinobi with the mobile communication device has on glasses. In the manga, he doesn't wear glasses.
 * In Shippūden episode 265, there are several changes:
 * The Konoha-nin behind Tajiki's comrade has a scar under his left eye. In the manga, none is present.
 * When Guy and Lee attack Haku with the Leaf Coiling Whirlwind in the manga, Lee is on the right and Guy is on the left. In this episode, they are reversed.
 * In the manga, when Mū is detected by Gaara's Concealed Sand Picture Cat, sand rises up from the ground and encircles Mū's foot. In the anime, sand is instead seen blowing about on the battlefield.
 * In Shippūden episode 267, there are a few errors:
 * The Gold and Silver Brothers are depicted without the plating on the bridge of their noses.
 * Mifune and his squad are seen running in the opposite direction than they were in the manga.
 * In Shippūden episode 269, there are a few errors/changes:
 * Ginkaku and his brother Kinkaku were both seen with whisker-like marks on their faces before they were even consumed by Kurama.
 * After Darui escaped from Benihisago, he is seen without his bandage on his right hand before he attacked Kinkaku.
 * When not battling, Ginkaku uses the rope to hold his gourd until it goes around Kinkaku's arm for battle. However, in one scene, after they started fighting, despite Kinkaku being seen wearing the rope, said rope is also shown around Ginkaku's neck.
 * When the flashback shows Kinkaku and Ginkaku jumping into Kurama's mouth, Ginkaku's purple shirt briefly flashes white.
 * When Ginkaku seals Samui, he is standing up. In the manga, he had been knocked away by Darui's attack, and was still sitting down when he sealed her.
 * The episode has Kinkaku smirking a lot while he is usually seen frowning in the manga.
 * There are a few errors in Shippūden episode 270:
 * The number of shinobi being strangled by Kakuzu was dropped from four to three.
 * In the manga, Chōza stopped Kinkaku's tail with one hand while in the anime, he used two.
 * At the Allied Shinobi Forces' headquarters when the Sensing Water Sphere was shown, no water was seen beneath it.
 * In the manga, Kitsuchi's punching of Kinkaku is shown from left to right. In the episode, the punch is shown from right to left. Also, more of his rock-transformed arm was visible in the manga while in the anime, his sleeve covered it.
 * In Shippūden episode 272, there are a few errors:
 * The Sunagakure-nin that was with the Fifth Division samurai was not wearing a mask. The manga, however, shows otherwise.
 * The Animal and Human Paths are depicted with longer bangs than in the manga. The Preta Path who should have been as short as the Animal Path, is depicted much taller.
 * In Shippūden episode 273, Izumo and Kotetsu's Kunai Blades are depicted without the weight in the middle of the chain.
 * In Shippūden episode 274, there are a few errors:
 * When Kurenai Yūhi and her and Asuma's child were seen, the village was in the backdrop. The anime dropped this in favour of a two-toned backdrop.
 * In the manga, when Chōza protected the current Ino-Shika-Chō generation from Asuma's Fire Release: Ash Pile Burning technique, he threw himself in front of them horizontally. In the anime, he stood in front of them.
 * In the manga, the kunai wielded by Asuma were depicted with square tips. In the anime, however, they were circular.
 * In the anime, when Asuma told his students that their formation had been perfected, tears came to their eyes. In the manga, though visibly saddened, they did not cry.
 * In Shippūden episode 275, there are a few errors/changes:
 * When Naruto enters Sage Mode and charges at his protection detail, only the two Akimichi are flung out, whereas in the manga, everyone was thrown out from behind the waterfall. Additionally, Naruto attacked them with his fists instead of kicking them.
 * In addition to this, Shibi was supposed to have sent his kikaichū to corner Naruto before he escaped from behind the waterfall, but this was omitted.
 * In a reverse predicament when A elbowed B in the manga, B spat up what appeared to be saliva. In the anime, however, B coughed up blood.
 * In Shippūden episode 298 when Killer B slices through Itachi Uchiha's Fire Release: Great Fireball Technique, Samehada is still bandaged up. However, in the manga, the greatsword was only partially bandaged.
 * In Shippūden episode 299 when Itachi impaled Nagato with his Totsuka Sword, the three shinobi are seen standing beside Susanoo. In the manga, however, they are all in front of it.
 * In the manga, Dodai's eye-patch is circular, while in the anime, it is depicted as being square.
 * In the manga, when the Third Raikage breaches through Dodai's Lava Release: Rubber Wall, the cut made to the wall is clean. In Shippūden episode 301, the cut is rough.
 * In the manga, during the scene where it shows the Third Raikage fallen on his own technique, he is depicted as younger. In Shippūden episode 301, they add age lines around his face.
 * In the manga omake tie-in, Shikamaru hair did not have his ponytail in the men's public bath. In the adapted anime episode, he has his ponytail the entire time there.
 * When Ōnoki explains his strategy with Mei Terumī and A, the Raikage's mouth is moving instead of the Tsuchikage's.
 * In Shippūden episode 326, there are a few errors/changes:
 * In the manga, when Sasuke kills White Zetsu, his Susanoo Sword is made of Amaterasu. In the anime, it is made of the same ethereal substance Susanoo is made of.
 * In the manga, when Sasuke emerges from the Mountains' Graveyard, his Sharingan is activated. In the anime, his Sharingan is not activated.
 * In Shippūden episode 331, Sasuke's Susanoo is positioned at the right and attacks to the left. In the manga, it is positioned at the left and attacks to the right.
 * In Shippūden episode 341, when we see Kinkaku and Ginkaku eating Kurama's flesh, Kinkaku is on the left-hand side and Ginkaku on the right. In the manga, it was reversed.
 * In chapter 584, Kabuto wears his usual outfit including his Konoha forehead protector. In Shippūden episode 336, he wears a purple hooded mantle.
 * In chapter 585, Itachi uses his Susanoo's curved blade to pin down Kabuto's construct of Orochimaru. In Shippūden episode 337, Itachi's Susanoo instead uses the Sword of Totsuka.
 * In chapter 605, the Kirigakure shinobi that tried to secure Rin Nohara's body was first skewered by Obito's Wood Release: Cutting Technique and was subsequently beaten to death. In the anime, two shinobi were attempting to secure Rin, with the first of them being killed by Obito's Wood Release and the second being beaten to death.
 * In episode 365, Sasuke's view of Konoha is seen from an angle to his left side, while in the manga it was seen from his right side.
 * In the manga, the chakra cloaks Naruto provides the rest of the Allied Shinobi Forces has the same yellow colour as his Nine-Tails Chakra Mode. In the anime, it looks like his original, red chakra Version 1 cloak.
 * In the manga, Kurama's eyes had the same pattern up the Sharingan the entire battle due to it being controlled.  In the anime, up until Kurama was equipped with Susanoo, its eyes were normal.
 * In the manga, Butsuma punched Hashirama with his left hand, where as in the anime, he is seen punching him with his right hand.
 * In the manga, Tobirama is wearing his usual armour in Hashirama's retelling. In Shippūden episode 368, he's wearing a variant with no shoulder guards.
 * In the manga, the two shadow clones Tobirama created were forming the clone seal as well. In the anime, they stood normally instead.
 * In the manga, Obito's Truth-Seeking Ball quickly dissolves the arm of Sasuke's Susanoo when it intercepts his attack. In the anime, it appears to successfully block the attack.
 * In the manga, after Obito produces chakra receivers to perform the Six Red Yang Formation, the Truth-Seeking Ball behind his right hand permanently disappears. In the anime, the ball remains behind his hand.
 * In the manga of chapter 652, Obito's imagination of his life had he returned to Konoha depicted his mask barely covering from his head to just below his right eye. In the anime of Shippūden episode 384, his mask almost covers the entire left portion of his face.
 * In the manga, when Hashirama used his Wood Dragons to restraint Madara, they were generic dragons. In the anime, they were the dragons with trunk-like nose.
 * In the coloured manga release of the chapter, the Sage Art: Magnet Release Rasengan is coloured similar to Shukaku's body, giving it the appearance of a sandy sphere. However, in the anime, the Magnet Release Rasengan is coloured in blue with Shukaku's cursed seal markings.
 * In the manga, the Forbidden Individual Curse Tag technique is black in colour with a Rinnegan-like symbol on it, while in the anime, it is white with a red, white, and teal symbol.
 * In the manga, Minato is erroneously depicted with six Truth-Seeking Ball's on his coat, while in the anime, it's corrected to five balls.
 * In the manga, within Hinata's Infinite Tsukuyomi dream, Hanabi's appearance is the one from Part I, while in the anime, it was corrected to her Part II design.
 * In the manga, Naruto sends Kaguya's severed arm with Black Zetsu inside it flying by punching it into the range of the Six Paths — Chibaku Tensei. In the anime, he swings it around several times before throwing it away.
 * In episode 477, Kakashi was incorrectly depicted with a Konohagakure headband at one time. The same episode erroneously showed Naruto missing his whisker markings once as well.