As a teenager, Henson began working for his father, doing puppet work on "The Great Muppet Caper" (1981). He continued working with the company after dropping out of the University of Colorado, toiling as puppeteer on such films as "Return to Oz" (1985), "Santa Clause: The Movie" (1985), "Little Shop of Horrors" (1986) and "Teenage Mutant Ninja Turtles" (1989). But Henson was 27 with virtually no producing credits when he was thrust into the presidency of the family company. There were several difficult years and many in the business thought him ill-equipped for the role, or simply as green as Kermit the Frog. Henson proved them wrong and has a resume brimming with credits of his own. In 1990, he won a Daytime Emmy for directing an episode of a children's series "Jim Henson's Mother Goose Stories" (The Disney Channel) and also served as executive producer, episodic director, and puppeteer on the ABC series "Dinosaurs" (1990-93), executive produced the short-lived series "Jim Henson's Dog City" (Fox, 1992), and "Jim Henson's Secret Life of Toys" (The Disney Channel, 1994). In 1996, Henson oversaw the critically praised but short-lived "Aliens in the Family" (ABC), a sort of intergalactic "The Brady Bunch" wherein an earthling and an extraterrestrial marry and raise their bi-planet brood of kids. Also that year, The Muppets returned to TV prominence with "Muppets Tonight!" (ABC).

Henson first produced and directed for the big screen with "The Muppet Christmas Carol" (1992) and performed similar duties on "Muppets Treasure Island" (1996). Breaking away from Kermit and Miss Piggy, the company produced "Buddy" (1997) about a socialite (Rene Russo) who raises a gorilla as her son.