The project originated after Gainax's planned film 'Aoki Uru' (a sequel to Royal Space Force) was cancelled in 1993 due to financial issues, prompting Hideaki Anno to finally create his own original TV series.

Anno initially wanted the production to be based at another studio like Sunrise, but ultimately pitched the project back to Gainax itself, which accepted it.

The show's early concept had 28 Angels instead of 17, and the working title during development was 'Jinzō Ningen Evangelion' (Artificial Human Evangelion); an earlier rejected title candidate was 'Alcion' before 'Evangelion' was chosen because character designer Yoshiyuki Sadamoto felt it sounded stronger with its diacritical mark.

Anno originally intended to connect the series' universe with his previous show 'Nadia: The Secret of Blue Water,' including making Second Impact analogous to an event from Nadia, but this was abandoned because NHK, which owned Nadia's rights, would not grant permission.

Character designer Yoshiyuki Sadamoto persistently argued against Anno's initial idea of making the protagonist a girl (in the vein of Gunbuster), eventually convincing Anno to make the lead a boy, Shinji Ikari.

Anno was such a fan of 'Sailor Moon' that he cast Kotono Mitsuishi (voice of Sailor Moon) as Misato Katsuragi, named Rei Ayanami after the Sailor Moon character Rei Hino, and cast Megumi Ogata as Shinji after seeing her performance in a Sailor Moon movie.

Anno was deeply influenced by Go Nagai's works, stating the ending of the film version 'had to become Devilman,' and that Eva's entry plug concept was essentially a modern take on Mazinger Z's 'Pilder On' system.

At the start of the broadcast, only about half of the episodes had been storyboarded and just a handful of episodes were fully completed, forcing the remaining 14 episodes to be finished in about half a year under a very tight schedule.

Episode 11 was outsourced to Studio Ghibli staff, resulting in a noticeably different, more comedic and lighter art style and character portrayal compared to other episodes.

The controversial final two episodes, which abandoned conventional plot resolution for an introspective psychological narrative, provoked massive backlash from fans expecting a traditional ending, most notably a scathing critique by Eiji Otsuka published in the Yomiuri Shimbun calling it 'exactly like a self-help seminar.'

The ending theme 'Fly Me to the Moon' was used in 14 different musical arrangements throughout the series, sung by various artists including opening vocalist Yoko Takahashi and voice actress Megumi Hayashibara (credited as 'Rei'), despite the visual animation always showing the same simple scene of Rei Ayanami rotating underwater.

The opening theme 'A Cruel Angel's Thesis' was originally meant to be written by a different lyricist, but producer Toshimichi Otsuki ended up commissioning Neko Oikawa by chance when her manager visited King Records for unrelated business; singer Yoko Takahashi was likewise asked to perform it on the spot after coming in to record 'Fly Me to the Moon.'

The soundtrack album 'Neon Genesis Evangelion III' reached number one on Oricon's weekly album chart in June 1996, the first anime soundtrack to do so in 17 years since Galaxy Express 999.

Due to a New Year's schedule conflict, episode 14 aired at 8:30 am on TV Tokyo instead of its regular evening slot, causing many viewers to miss it and resulting in the lowest recorded rating of the series (0.9%).

Anno described the deadlock over how to end the story as needing to choose between three ways to 'fold up a spread-out furoshiki cloth': folding it properly, tearing it, or just throwing it away — and said Evangelion chose to 'tear it and throw it away.'