The studio was founded in 2003, later becoming formally incorporated in 2006 by former employees of Gonzo, and has contributed to various anime series and films.

[2] Its name is derived from the Japanese word for "three-dimensional" (三次元, sanjigen).

Sanzigen joined the Japanese joint holding company Ultra Super Pictures with studios Ordet and Trigger, that would later be joined by Liden Films.

On 13 December 2019, Bushiroad announced that it had acquired 8.2% of Sanzigen.

Ultra Super Pictures now owns 75.4% of Sanzigen and studio president Hiroaki Matsuura owns 16.4% of the company.