| Brats (2024)As Self (archive footage) (uncredited) | (Not seen) |
| Daddio (2023)As Clark | (Not seen) |
| Asphalt City (2023)As Gene Rutkovsky | (Not seen) |
| Licorice Pizza (2021)As Jack Holden | (Not seen) |
| Flag Day (2021)As John Vogel | (Not seen) |
| The Professor and the Madman (2019)As Dr. William Chester Minor | (Not seen) |
| The Angry Birds Movie (2016)As Terence (voice) | (Not seen) |
| The Gunman (2015)As Terrier | (Not seen) |
| The Secret Life of Walter Mitty (2013)As Sean O'Connell | (Not seen) |
| Gangster Squad (2013) (AKA "L.A. Gang Story")As Mickey Cohen | (Not seen) |
| Americans (2012)As Commie | (Not seen) |
| This Must Be the Place (2011)As Cheyenne | (Not seen) |
| The Tree of Life (2011)As Jack O'Brien | (Not seen) |
| Phil Ochs: There But for Fortune (2010)As Self | (Not seen) |
| I'm Still Here (2010) (AKA "I'm Still Here: The Lost Years of Joaquin Phoenix")As Himself | (Not seen) |
| Fair Game (2010)As Joseph Wilson | (Not seen) |
| The People Speak (2009)As Himself | (Not seen) |
| What Just Happened (2008)As Himself | (Not seen) |
| Milk (2008)As Harvey Milk | (Not seen) |
| War Made Easy: How Presidents & Pundits Keep Spinning Us to Death (2007) (AKA "War Made Easy") | (Not seen) |
| Persepolis (2007) | (Not seen) |
| All the King's Men (2006) (AKA "Das Spiel der Macht")As Willie Stark | (Not seen) |
| The Interpreter (2005)As Tobin Keller | (Not seen) |
| The Cutting Edge: The Magic of Movie Editing (2004)As Self | (Not seen) |
| The Assassination of Richard Nixon (2004)As Samuel Bicke | (Not seen) |
| Pauly Shore Is Dead (2003)As Himself | (Not seen) |
| It's All About Love (2003)As Marciello | (Not seen) |
| 21 Grams (2003)As Paul Rivers | (Not seen) |
| Mystic River (2003)As Jimmy Markum | (Not seen) |
| I Am Sam (2001)As Sam Dawson | (Not seen) |
| A Constant Forge (2000)As Self | (Not seen) |
| Up at the Villa (2000)As Rowley Flint | (Not seen) |
| Before Night Falls (2000) (AKA "Antes que anochezca")As Cuco Sanchez | (Not seen) |
| The Weight of Water (2000)As Thomas Janes | (Not seen) |
| Sweet and Lowdown (1999)As Emmet Ray | (Not seen) |
| Being John Malkovich (1999)As Himself (uncredited) | (Not seen) |
| Hurlyburly (1998) (AKA "Casting Director")As Eddie | (Not seen) |
| The Thin Red Line (1998)As 1st Sgt. Edward Welsh | (Not seen) |
| She's So Lovely (1997)As Eddie Quinn | (Not seen) |
| Hugo Pool (1997) (AKA "Pool Girl")As Strange Hitchhiker | (Not seen) |
| The Game (1997)As Conrad Van Orton | (Not seen) |
| U Turn (1997) (AKA "Stray Dogs")As Bobby Cooper | (Not seen) |
| Dead Man Walking (1995)As Matthew Poncelet | (Not seen) |
| Carlito's Way (1993)As David Kleinfeld | (Not seen) |
| State of Grace (1990)As Terry Noonan | (Not seen) |
| We're No Angels (1989)As Jim | (Not seen) |
| Casualties of War (1989)As Sgt. Tony Meserve | (Not seen) |
| Judgment in Berlin (1988)As Guenther X | (Not seen) |
| Colors (1988)As Officer Danny McGavin | (Not seen) |
| At Close Range (1986)As Bradford "Brad" Whitewood Jr. | (Not seen) |
| The Falcon and the Snowman (1985)As Daulton Lee | (Not seen) |
| Bad Boys (1983)As Mick O’Brien | (Not seen) |
| Fast Times at Ridgemont High (1982)As Jeff Spicoli | (Not seen) |
| Taps (1981) (AKA "The Siege at Bunker Hill: T.A.P.S")As Cadet Captain Alex Dwyer | (Not seen) |