Hanna-Barbera originally asked comic artist Doug Wildey to design a series starring the radio drama hero Jack Armstrong, the All-American Boy, but when the studio could not secure the rights, Wildey reworked the concept into Jonny Quest overnight.

For inspiration, Wildey drew on Jackie Cooper and Frankie Darro movies and Milton Caniff's comic strip Terry and the Pirates, while producer Joe Barbera pushed him to incorporate elements from the James Bond film Dr. No, including a '007'-style code number for Dr. Quest in the first episode titled 'Jonny Quest File 037'.

Wildey used contemporary science magazines like Popular Science, Popular Mechanics, and Science Digest to imagine technology 10 years in the future, devising devices like a 'snowskimmer' and hydrofoils for the show.

Wildey said Hanna-Barbera refused to give him a full 'created by' credit, settling instead on the credit 'based on an idea created by' him.

The show's working titles included 'The Saga of Chip Baloo' and 'Quest File 037'; the final name Quest was picked from a phone book for its adventurous connotations.

Although Race Bannon's visual design was modeled after actor Jeff Chandler, his name was created by combining 'Race Dunhill' and 'Stretch Bannon' from an earlier comic strip.

Wildey wanted Jonny's pet to be a monkey, but Hanna-Barbera overruled him in favor of the dog Bandit, who was designed not by Wildey but by animator Richard Bickenbach.

Although they never appear in any actual episode, footage from the earlier Jack Armstrong test film—showing Jack Armstrong and Billy Fairfield escaping African warriors by hovercraft—was reused in the Jonny Quest closing credits.

Despite being an almost instant critical and ratings success, Jonny Quest was canceled after just one season because its high production costs made ABC reluctant to commit to further episodes, even though producer William Hanna wanted to continue.

Jonny Quest is one of only a few American TV series, alongside Hanna-Barbera's The Jetsons, to have aired on all three major U.S. television networks (ABC, CBS, and NBC).