Voiced by: Samuel L. Jackson
Perhaps the most debated character within the story, "Ninja" is Afro's complete antithesis, always speaking and usually saying aloud what Afro can't bring himself to say; generally, Afro refuses to respond to anything he says other than telling Ninja Ninja to "shut up." As his name implies, he dresses in a ninja motif. He also seems to have a counter color scheme to Afro, while also having a similar frame and haircut though he slouches when he walks. This can best be seen at the end of episode 2, where they are walking side by side after the fire. There are several clues throughout the show that point to Ninja Ninja being imaginary, such as Afro being the only one who speaks to him, his constant disappearing when Afro is in combat or internal conflict, and the fact he is not hurt when he and Afro are knocked off a cliff by an RPG despite being next to each other. It is later shown in Episode 4 that Ninja Ninja first appeared suddenly when Afro lost his friends and loved ones while obtaining the Number Two headband. At the beginning of Episode 5, it is revealed that Ninja Ninja was the one that was "killed" by Kuma's strike; a symbolic way of showing that Afro has come to terms with the loss of his friends at this point in his journey. Also about halfway through the episode when Afro finally meets Justice again, Justice states that he watched him shed his imaginary friend (Ninja).
In the collector's DVD, interviews with the staff and writers concede that Ninja Ninja is indeed imaginary. However, even though Ninja Ninja is 'imaginary', he appears to have some form of presence in the real world, as well. When Brother 2 of the Empty Seven spies on Afro, Ninja Ninja can be clearly seen from Brother 2's point of view through the binoculars. Ninja Ninja also interacts with items around him constantly such as catching Afro's joint in his mouth, moving a hanging pillar inside Okiku's home, putting Okiku's comb into Afro's afro, eating the food that was intended for Afro given by Brother 3 (in the Director's cut) and throwing the Afro droid's microchip at Afro to cut in two. The idea of Ninja Ninja having at least a partial existence in reality is once again brought into light when he is 'killed' by Kuma. Because Kuma was such a skilled warrior and had the intent to kill Afro on the sword strike that killed Ninja Ninja, it would seem odd that he would pause from his attack and have a conversation with Afro if there was not a reason to give pause, which strengthens the idea that he was taken back by Ninja Ninja's sacrifice before attacking Afro again. However, in Ninja Ninja's final conversation with Afro, it is clear that the words spoken by Afro to Ninja Ninja are heard and understood by Kuma as referring to him, implying that the pause and Ninja Ninja's death are mostly Afro's mental constructs.
At the show's website, Ninja Ninja can be seen in the background, behind Afro, during the final seconds of the trailer. How he has managed to come back for the sequel after being "killed" has yet to be revealed, but his return does imply that he was in fact imaginary.