The studio was founded as Daicon Film in the early 1980s by university students Hideaki Anno, Yoshiyuki Sadamoto, Takami Akai, Toshio Okada, Yasuhiro Takeda and Shinji Higuchi. Their first major projects were two animated shorts produced for the Japan National SF Convention in 1981 and 1983 which firmly established the studio as a talented new anime production company. The studio was renamed Gainax in 1985.

Their first feature project was Royal Space Force: The Wings of Honneamise, released in 1987 to critical acclaim but tepid commercial performance. A sequel was proposed in 1992 but was scrapped for lack of funding. Their next release was the more financially successful OAV series Gunbuster in 1988. Since then, Gainax has produced several other well-known titles, such as Nadia: The Secret of Blue Water, Otaku no Video, the acclaimed OVA series FLCL and their most popular series to this day, the highly influential Neon Genesis Evangelion, while producing other items such as garage kits and adult video games to keep them financially stable.

Following the success of Evangelion, Gainax president Takeji Sawamura was arrested on charges of corporate tax evasion, forging costs for the company's software products in 1996 and 1997 and neglecting to report more than 1.5 billion yen in company income.

The studio is mostly known for their in-house productions, but has also produced anime adaptations of His and Her Circumstances and Mahoromatic.

In 2004, the studio released Diebuster, a sequel OAV to Gunbuster for their twentieth anniversary, as well as This Ugly Yet Beautiful World in conjuction with the Shaft studio.

Gainax's most recent projects include two successful TV series from director Hiroyuki Imaishi--the 2007 mecha anime Gurren Lagann and the 2010 comedy series Panty & Stocking with Garterbelt. They are also working in conjuction with Anno's new Studio Khara on four new Evangelion feature films, the first of which was released in fall of 2007.

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• Nadia: The Secret of Blue Water (1990)
  
• Neon Genesis Evangelion (1995)
  
• His and Her Circumstances (1998)
  
• Mahoromatic (2001)
  
• Petite Princess Yucie (2002)
  
• Magical Shopping Arcade Abenobashi (2002)
  
• This Ugly Yet Beautiful World (2004)
  
• Gurren Lagann (2007)
  
• Shikabane Hime (2008)
  
• Panty & Stocking with Garterbelt (2010)
  

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• Royal Space Force: The Wings of Honneamise (1987)
  
• Neon Genesis Evangelion: Death and Rebirth (1997)
  
• Neon Genesis Evangelion: The End of Evangelion (1997)
  
• Evangelion 1.0: You Are (Not) Alone (2007; animation by Studio Khara)
  
• Evangelion 2.0: You Can (Not) Advance (2009; animation by Studio Khara)
  

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• Gunbuster (1988)
  
• Otaku no Video (1991)
  
• FLCL (2000)
  
• Diebuster (2004)