The Yu-Gi-Oh! 5D's manga is a spin-off of its anime series. Like the Yu-Gi-Oh! GX manga, the events that take place, as well as the cards used by characters differ from those in the anime. It was published monthly in the V Jump magazine in Japanese, and has been released in English via the Shonen Jump magazine starting with the January 2011 issue. It began serialization on August 21, 2009, and ended on January 21, 2015, with a bonus chapter being announced to be included in the final volume. The author of the manga is Masahiro Hikokubo and the artist of the manga is Masashi Satō. The manga is supervised by Kazuki Takahashi.

Em uma versão alternativa de Yu☆Gi☆Oh 5D's, Yuusei e seu amigo, Sect, estão duelando em Satellite quando um Cavaleiro Esqueleto de uma lenda urbana aparece, forçando Yuusei a duelar com ele pela liberdade de Sect. Em Neo-Domino, Rex Godwin está planejando um torneio conhecido como o Grand Prix D1 enquanto Jack se dirige para Satellite e confronta Yuusei, que nesta versão, parece não saber...