After the cancellation of Star Trek: The Original Series in 1969, its unexpected popularity in syndication led Gene Roddenberry to continue the franchise in animated form, which allowed for spectacular imagery and non-humanoid aliens impossible to depict practically in live action.

An early proposal from Filmation and Paramount envisioned the original cast training a teenage crew aboard a ship called Excalibur, including a Vulcan named Steve, an African-American boy named Bob, and a Chinese boy named Stick, but this concept was phased out due to a bitter relationship between Roddenberry and Paramount.

Pavel Chekov did not appear in the series because the budget couldn't afford the full original cast; he was replaced by the three-armed, three-legged alien Lieutenant Arex, while the cat-like Lieutenant M'Ress sometimes filled in for Uhura.

Leonard Nimoy refused to voice Spock unless George Takei and Nichelle Nichols were hired, after noticing their absence at the first recording session; producer Lou Scheimer admitted they had unintentionally slighted the show's only two minority actors, and both were quickly cast.

To make up for cutting Walter Koenig from the cast, Filmation bought a script from him for the episode 'The Infinite Vulcan.'

William Shatner and Leonard Nimoy, both touring in stage plays at the time, recorded their voice lines wherever they happened to be performing and had the tapes shipped to the studio.

Animators rotoscoped the Enterprise and original cast from 35mm footage of The Original Series, enlarging the uniform chevrons to make them easier to animate, and cut costs by using stock footage, silhouetted action scenes, and having characters cover their mouths to avoid animating lip movement.

The animated series used a new theme credited to pseudonyms 'Yvette Blais' and 'Jeff Michael' instead of Alexander Courage's original theme, because Courage, in a long-running royalty feud with Roddenberry, refused to allow reuse of his composition.

Writer David Gerrold gave Captain Kirk the middle name 'Tiberius' in the animated series, inspired by I, Claudius; he only learned in 2014 that Roddenberry's earlier series The Lieutenant had also featured a character named William Tiberius Rice.

Because George Takei was running for a Los Angeles city council seat, the FCC's equal-time rule prevented the series premiere from airing in the Los Angeles market, as station KNBC feared it would have to offer equal airtime to his opponents.