Henson provided the voices of Hoggle, one of the main characters in Labyrinth (1986) and Jack Pumpkinhead in Return to Oz (1985). He was the Dog in both versions of The Storyteller (1988 and 1990) and Dr. Phil van Neuter, the Muppet mad scientist who tries to suck out Gonzo's brain, in Muppets from Space (1999).

He has also taken over the roles of the Muppets Scooter and Janice since the death of Richard Hunt in 1992.

He directed The Muppet Christmas Carol in 1992 and Muppet Treasure Island in 1996, the first Muppet films produced after Jim Henson's death.

He was the producer of the TV series Dinosaurs, Aliens in the Family, and Bear in the Big Blue House. His most visible recent project was the cult sci-fi series Farscape.

Henson is the co-creator, producer and currently a performer in the Off-Broadway puppet-based variety show geared towards adults called "Stuffed and Unstrung."

Henson is co-producing The Power of the Dark Crystal and The Movie.