Feature Films
- Being John Malkovich (1999)
- Human Nature (2001)
- Confessions of a Dangerous Mind (2002)
- Adaptation (2002)
- Eternal Sunshine of the Spotless Mind (2004)
- Synecdoche, New York (2008)
- Anomalisa (2015)
- I'm Thinking of Ending Things (2020)
- Orion and the Dark (2024)
Plays
- Hope Leaves The Theater (2005)
- Anomalisa (2005, written as 'Francis Fregoli')
Short Films
- Jackals & Fireflies (2022)
Novels
- Antkind (2020)
- Untitled (upcoming)
Unproduced, Rumoured, Upcoming
- Hounds of Eyelids (formerly Oklahama!) (Based on the 1978 novel IQ83 by Arthur Herzog. Intended to be a film, there's been talk that Kaufman may turn this into a limited run TV series.)
- The Memory Police (Based on the 1994 novel by Yōko Ogawa. Directed by Reed Morano)
- A Scanner Darkly (Unproduced)
- How and Why (TV. A pilot was filmed but never aired.)
- Frank or Francis (Unproduced)
- Chaos Walking - The Knife of Never Letting Go (2019) (Adaptation of Patrick Ness' YA novel. Kaufman wrote a draft, which was then re-written by several hands. The finished film has essentially no relation to Charlie's script.)
- Depressed Roomies (TV, unproduced)
- Ramblin' Pants (TV, unproduced)
- Slaughterhouse Five (was in talks to write this for Guillermo del Toro)
