For Disney, he is best known for providing the voice of Pain in Disney's 1997 animated feature film, Hercules, a role he later reprised in the television series, House of Mouse, Sorcerers of the Magic Kingdom, and World of Color: Villainous. He would portray the Adrenal Gland in Cranium Command at Epcot. He also voiced Nosy in Lilo & Stitch: The Series and its 2006 film, Leroy & Stitch. Additionally, he voiced XL in Buzz Lightyear of Star Command, Fish Santa in Fish Hooks, Dickie in Randy Cunningham: 9th Grade Ninja, and Dr. Wolfman in Future-Worm!. He even portrayed Yogi Paxil in Encino Woman.
In 1998, Goldthwait directed the unaired pilot of The Aquabats!, produced for Buena Vista Television and based on the real-life band of the same name. Buena Vista ultimately did not produce a full series, and the show would eventually be produced 14 years later as The Aquabats! Super Show! for Hub Network.