The Manga adaption of the Phi Brain: Kami no Puzzle series began serialization in Kadokawa Shoten's Newtype Ace magazine in November 11, 2011. It is written by Hajime Yadate and illustrated by Yoshiki Togawa. The manga ended on September 10, 2012, with a total of 2 volumes.

Another Manga adaption named Phi Brain: Saigo no Puzzle (ファイ・ブレイン 最期のパズル, lit. meaning  Phi Brain: The Last Puzzle) was published between April 27, 2011 and October 12, 2011 in the Weekly Shounen Magazine. It was written and ilustrated by Haruo Ueno.

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