Shinseiki Evangelion is based on the anime series but with several differences, written and illustrated by its character designer Yoshiyuki Sadamoto. It was initially serialized in Shounen Ace, but moved to Young Ace on July 7, 2009. Although it was set to be released just shortly before the anime series began airing, production delays pushed the anime's airing date to 10 months after.

The series was published in English as Neon Genesis Evangelion by VIZ Media from December 1998 to May 2003 for seven volumes, it was later reprinted under the Action imprint label from February 25, 2004 to February 10, 2015 and in 3-in-1 omnibus edition's from November 13, 2012 to June 14, 2016, with the latter volume released in 2-in-1 format.

It was also published in Spanish as Neogénesis Evangelion by Norma Editorial in comic-book format since July 1997 until it was cancelled in July 2008, which was later published in the original 14-volume format from May 2003 to January 2015; in Brazilian Portuguese by Jbc from October 2011 to November 2014; and in Italian by Panini Comics under the Planet Manga imprint in comic-book format from November 1, 1997 to November 22, 2014, which was later published in the original 14-volume format from October 18, 2001 to November 22, 2014.