Thorton had his first break when he co-wrote and starred in the 1992 thriller One False Move. He also appeared in several major film roles in the 1990s, including Oliver Stone's neo-noir U Turn, Primary Colors, and A Simple Plan, which earned him his third Academy Awards nomination. Additionally, he voiced Jack in DreamWorks' Puss in Boots.
For Disney, he portrayed Karl Childers in the 1996 drama film Sling Blade, for which he won an Academy Award for Best Adapted Screenplay and was nominated for an Academy Award for Best Actor. He also played Harry S. Stamper in the 1998 sci-fi disaster film Armageddon and Willie T. Stokes in the 2003 black comedy film Bad Santa. and voiced Jiko-bō in Princess Mononoke.