Alex Kurtzman first mentioned a youth-focused animated Star Trek series in January 2019, shortly after the announcement of the adult animated series Star Trek: Lower Decks, envisioning it as tonally and visually distinct from that show.

Nickelodeon ordered two full seasons of Prodigy in April 2019 due to the amount of animation work required, and the series was designed to premiere on Paramount+ before later airing on Nickelodeon.

Kate Mulgrew was approached about reprising Kathryn Janeway a year before her involvement was officially announced, and Kurtzman was surprised the news never leaked during that time; Mulgrew was initially reluctant but was won over by the idea of introducing Star Trek to a new generation.

The character Murf was originally created as a joke—a 'semi-sentient blob' that had randomly joined the crew—but the writers grew fond of the idea of a dog-like character for young viewers and later gave Murf a real character arc.

John Noble's villain character the Diviner was directly inspired by Ricardo Montalbán's performance as Khan Noonien Singh, and his initial appearance floating in a tank was inspired by the Guild Navigator creature from David Lynch's 1984 film Dune.

Jimmi Simpson described his robotic character Drednok as essentially a more talkative version of Maximilian, the robot villain from the 1979 film The Black Hole.

Nami Melumad became the first woman to compose the score for a Star Trek series, working under the guidance of Michael Giacchino, who composed the show's main theme and advised her not to overuse it so it would feel earned when it appeared.

Composer Nami Melumad gave each main character their own musical motif, such as a trombone for the clumsy Jankom Pog, a piccolo for Zero, and a bell-toned keyboard sound for Gwyn.

The series was made as CG animation rather than the traditional 2D style of earlier Star Trek animated shows, with designs first developed as 2D drawings before being rendered in 3D; Kurtzman compared its visual quality to the anthology series Love, Death & Robots and claimed it was feature-film quality.

Despite winning two Children's and Family Emmy Awards and receiving a 94% Rotten Tomatoes score for season one and 100% for season two, Paramount+ canceled Prodigy in June 2023 as part of a wider cost-cutting purge before Netflix picked it up for streaming.