The series' true origin came from Cartoon Network wanting a Superman-centric show to premiere around the time of the film Superman Returns; when Cartoon Network passed on the project, Kids' WB! picked it up with the same Superman-focused concept.

Producer James Tucker clarified that, despite fan speculation, the series was never tied to the Justice League Unlimited episode 'Far From Home,' and Supergirl was never intended to join the Legion in this show.

Early reports suggested the series would be titled 'Superboy and the Legion of Super-Heroes,' but the official April 2006 announcement confirmed the title as simply 'Legion of Super Heroes,' with the character referred to as a young Superman rather than Superboy, possibly due to legal issues over Superboy's ownership.

A planned but ultimately canceled third season would have taken place three years after season two, introducing characters like Sensor, Magnetic Kid, Supergirl, Tellus, Princess Projectra, and Shadow Lass, and would have focused on Brainiac 5's redemption arc and Brainiac 6 trying to destroy the Legion; James Tucker also planned to adapt 'The Ghost of Ferro Lad' to introduce Ferro Lad's twin brother.

Brainiac 5's personality and design in the series were inspired by the version of the character from Dan Abnett and Andy Lanning's Legion of Super-Heroes comic series.

The tie-in comic book was titled 'Legion of Super-Heroes in the 31st Century' specifically to distinguish it from more youth-oriented DC titles such as Justice League Adventures and Superman Adventures.

The series was nominated for three Creative Arts Emmy Awards (Daytime Emmys) for music direction/composition and sound editing/mixing, but did not win any of them.

A 2007 McDonald's Happy Meal tie-in promotion included eight figurines of characters such as Superman, Timber Wolf, Lightning Lad, Brainiac 5, Bouncing Boy, Mano, Tharok, and Validus, while planned Mattel action figures were never produced due to lack of retailer interest.