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Dino De Laurentiis became a "ghost" producer on the series when Filmation developed monetary problems completing the animation involving the use of computers to create the spaceship animation, one of the first uses of computers in traditional animation. Since DeLaurentis was seeking the rights for the use of the Flash Gordon property for a live action film, and Filmation held the rights for all filmed media for the Flash Gordon characters, Filmation and DeLaurentis came to a deal. In exchange for the funding to complete the animation on the series, DeLaurentis would get the live action film rights to Flash Gordon while Filmation would retain the rights to animated projects featuring Flash Gordon.

This series was originally conceived as a live action film for television, but it soon became clear that live-action would be cost prohibitive, so an animated film was instead commissioned. The results were so well received that it was decided not to air it as a film, but instead as a series. The film was heavily re-edited to play as a weekly serial and many additional episodes were ordered. After the series was canceled, the original version of the film (which included a lengthy prologue and other scenes that were never seen in the series) aired under the title Flash Gordon: The Greatest Adventure of All (1982).

As the show was originally conceived for prime time rather than Saturday mornings, the first season was more violent and featured 'sexier' women than other Saturday-morning shows of the period. It also ran as an updated version of an old-style chapter play, with one overarching serialized story rather than separate, self-contained episodes. The second season was made more kid-friendly and abandoned the serialized format for two 11-minute mini-episodes, a miscalculation as the show's ratings then plummeted severely, leading to cancellation.

The fluent movements of the human characters were achieved by filming extensive live-action footage of human actors for rotoscoping. Filmation's effects department built models of the spaceships for the same purpose, painting them white and covering them in thin black lines. Using a computerized camera, the film negatives were printed as cels, creating "positive" versions of the ships for the animators to use in rotoscoping.

Alan Oppenheimer would later reuse Ming the Merciless's voice for Skeletor in Filmation's He-Man and the Masters of the Universe (1983). Princess Aura's character model was re-purposed for that of Teela, specifically her face and tiara, but with a shorter haircut.