The character Æon Flux was not originally meant to be a recurring part of the series; MTV pushed creator Peter Chung to keep her in it, despite her dying at the end of the first batch of shorts.

Creator Peter Chung intended the cartoon as a reaction to heroic Hollywood action films, not as a spoof, aiming to make audiences question the wider context of action heroes rather than simply parody them.

Æon Flux is considered the first American adult animated series to be a drama rather than a comedy.

In the original shorts, Æon Flux dies violently in almost every episode because Chung never intended to make more episodes and felt having her repeatedly die was the best narrative solution; she only 'dies' once in the later half-hour series.

Aside from the exclamation 'No!' in the pilot and the word 'plop' in the episode 'Leisure,' all the short episodes are completely devoid of intelligible speech, relying instead on sound effects like laughter, grunts, and sighs; dialogue was not used extensively until Season 3.

On the 2005 DVD release, the dialogue of the character Clavius in the episode 'Utopia or Deuteranopia,' originally voiced by Joseph Drelich, was re-recorded by series executive producer Japhet Asher.

Peter Chung also directed a live-action/animated Diet Pepsi commercial called 'Something Wrong?' starring Malcolm McDowell as a Trevor Goodchild-like character and Cindy Crawford as an Æon Flux-like character, made for Super Bowl XXX in 1996 but pulled and later aired exclusively on MTV.

Creator Peter Chung called the 2005 live-action movie 'a travesty,' saying watching its public screening made him feel 'helpless, humiliated, and sad,' and noted that the Æon Flux character, as he conceived her, does not actually appear in the film.

A 1996 PlayStation game based on the original animated series, loosely based on the episode 'The Demiurge' and developed by Cryo Interactive, was cancelled after Viacom New Media merged with Virgin Interactive; its assets were later reworked into the unrelated 1997 game Pax Corpus after being stripped of Æon Flux branding.