Board Thread:Theories and Speculation/@comment-1872728-20151019025302/@comment-734582-20151022195905

Georgio722 wrote: But if chakra is yellow/blue, then what's with the chakra colour of each individual? Naruto originally said (about the fox) "i can't explain, but if it were a color, my chakra would be blue, and Kyubi's red".

I think the Anime understood this to be literal (or just picked a color) and made it Blue. For animation simplicity, all chakra is identical in color.

I am not sure when Kishimoto first depicted Naruto's chakra as yellow. It's possible that Kishimoto only decided this when he made the Kurama Chakra mode, as Naruto's yellow + Kyubi's red is obviously Orange.

TLDR: every chakra has its own color, Anime just chose blue and for animation sake gives everyone the same color.