Gainax launched the project to create a movie ending for the series in 1997. They first released Death and Rebirth, consisting of a highly condensed character-based recap and re-edit of the TV series (Death) and the first half of the new ending (Rebirth). The project was completed later in the year, and released as The End of Evangelion; The End of Evangelion is an alternate viewpoint of the series ending, which supplements episodes 25 and 26. The three were compiled as a single movie, the Revival of Evangelion in 1998.

The two endings are similar in plot, but while in the film Shinji rejects Instrumentality, the television series ends after his decision is made but before it is clear which option he chose. In still frames in episodes 25 and 26, Unit 01 is depicted with wings and the corpses of Misato and Ritsuko are shown, hinting that these events had been planned. In the English-language Director's Cut version of episode 24, the preview of the next episode shows concept frames from the fight between Asuka and the mass-produced Evas, and the title of the next episode is presented as "Air", which is the title of the first chapter from The End of Evangelion, rather than showing scenes from the TV series ending as it does in the original cut. There was a sudden shift in tone around episode 16 of the series. This was partly due to scheduling restraints, which drastically reduced the number of frames that could be drawn for each episode, and partly due to the Sarin gas attack on the Tokyo subway on March 20, 1995, which occurred while the series was under production; Anno decided to remove elements of the series plot that he felt were too similar to the real-life attack. Anno stated before production that he did not know how the show would end, nor what would become of the characters. Reaction was decidedly mixed; reception of the latter quarter of the TV series had often been hostile to the point of death threats, and the movies were seen as being even more incomprehensible (such as the ending), bizarre and even disgusting.

In May 1998, Gainax was audited by the National Tax Agency at the urging of the Tokyo Regional Taxation Bureau: Gainax was suspected of committing tax evasion on the massive profits accruing from various Evangelion properties. Gainax had concealed 1.56 billion yen worth of income (thereby failing to pay 560 million yen due in corporate taxes) which it had earned between the release of Evangelion and July 1997. Gainax would pay companies closely related to it various large fees, ostensibly to pay for animation expenses, but then immediately withdraw 90% of the sums from the other company's accounts as cash and store it in safe deposit boxes (leaving 10% as a reward for the other company's assistance).

Eventually Takeshi Sawamura and tax accountant Yoshikatsu Iwasaki were arrested on 13 July 1999 for concealing income of 1.5 billion yen failing to pay corporate taxes of 580 million yen. Yasuhiro Takeda defends Sawamura's actions as being a reaction to Gainax's perpetually precarious finances and the shaky accounting procedures internally:

"Sawamura understood our financial situation better than anyone, so when Evangelion took off and the money really started rolling in, he saw it as possibly our one and only opportunity to set something aside for the future. I guess he was vulnerable to temptation at that point, because no one knew how long the Evangelion goose would keep laying golden eggs. I don't think he purposely set out with the goal of evading taxes. It was more that our level of accounting knowledge wasn't up to the task of dealing with revenues on such a large scale."

On September 9, 2006, Gainax confirmed a new animated film series called Rebuild of Evangelion, consisting of four movies to be released in 2007 and 2008. The first three movies will be an alternate retelling of the TV series (including new scenes, settings, backgrounds, characters), and the fourth movie will be a completely new conclusion to the story. The first of the new movies was released in Japan on September 1st, 2007 under the name Evangelion: 1.0 You Are (Not) Alone.

Development of a live-action movie version of Neon Genesis Evangelion was announced in May 2003 by the Houston-based anime distributor ADV Films, who holds worldwide rights to the series outside of Asia and Australia, and Universal Studios would be the American distributor. The film will be made by ADV, Gainax, and Weta Workshop Ltd.. Its release is currently projected to occur at any time ranging from as early as 2009 to as late as 2015. In December 2005, Fortune Magazine reported in an article about ADV Films that it had raised "about half of the $100 million to $120 million" needed to produce the film. It's not completely clear if this money was raised by ADV alone or if part of that amount was contributed by Gainax.

As of 2009[update], the project is considered to be in "development hell", as a director has yet to become available or announced officially. In a panel discussion at Tekkoshocon on April 2, 2006 featuring Matt Greenfield and wife Tiffany Grant, many aspects of the project were revealed. Greenfield recalled that Weta approached ADV about a live-action Eva movie after completing work on The Lord of the Rings film trilogy, but work was delayed by King Kong and The Chronicles of Narnia. It was revealed that three described "A-list" directors and several celebrities had approached the project, rather than the other way around, and the slug script was written by a writer of several other well-known science fiction movies (though this is subject to be rewritten and tailored to the director's vision). Greenfield also reiterated his belief that they did not want to make the movie for profit, but because they wanted to do it and have it done it right (as with Lord of the Rings), and promised effort toward a trilogy of Evangelion films (as opposed to trying to condense the story into one film and lose vast amounts of material), similar again to the Lord of the Rings trilogy.

Beyond these official announcements and some concept art produced by Weta Workshop, little or no more information about the film(s) has been made available. At Anime Expo 2008, ADV founders Matt Greenfield and John Ledford, in response to a question over the progress of the live-action film, revealed they had hired the producer for Appleseed Ex Machina, Joseph Chu, and pitched the idea to other producers such as Jerry Bruckheimer and Steven Spielberg. They went on to say that interest in the project had been boosted by the success of the 2007 film Transformers.