Shaft was founded on September 1, 1975 by Wakao Hiroshi who had previously worked for Mushi Production. The company was originally founded to paint the animation but later worked on animation production as a subcontractor. They were able to produce their own first original anime, Yume kara Samenai in 1987.

In 2000, after Shaft cooperating with Gainax to produce a DVD special of remastered Gunbuster, they were in joint production with Gainax to produce Mahoromatic, This Ugly and Beautiful World, and He is My Master. Wakao Hiroshi retired as the studio's representative director in 2004, and Kubota Mitsutoshi replaced him, with Wakao staying as a chairman of the studio.

Following Kubota's appointment, Shinbou Akiyuki was hired to act as the studio's executive director, which was to ensure that the company would be able to produce series in a unique "house style." Oonuma Shin and Oishi Tatsuya were invited by Shinbou to work with the company as well, and the three, nicknamed "Team Shinbo", defined the future of the studio with their artistic influences. Shinbou has since mentored several directors that have worked with the studio.

Oonuma left the company in 2009 to pursue a career with Silver Link, where he's taken a similar role to Shinbou's executive role with Shaft. In 2015, Shaft reorganized from a limited company to a joint-stock company.