Filmography
| Year | Title | Role |
| 2023 | Asphalt City (2024) | Gene Rutkovsky |
| 2021 | Flag Day (2021) | John Vogel |
| 2021 | Licorice Pizza (2021) | Jack Holden |
| 2019 | The Professor and the Madman | Dr. William Chester Minor |
| 2016 | The Angry Birds Movie | Terence |
| 2016 | The Last Face (2017) | Director |
| 2015 | The Gunman | Jim Terrier |
| 2015 | Sweet Micky for President | Actor |
| 2015 | The Three Hikers | Actor |
| 2013 | The Secret Life of Walter Mitty (2013) | Sean O'Connell |
| 2013 | Gangster Squad | Mickey Cohen |
| 2013 | The Human Experiment | Executive Producer, Narrator |
| 2011 | This Must Be the Place | Cheyenne |
| 2011 | The Tree of Life | Jack |
| 2010 | Fair Game (2005) | Joseph Wilson |
| 2008 | What Just Happened | Sean Penn |
| 2007 | Into the Wild (2007) | Director, Producer, Screenwriter |
| 2007 | War Made Easy: How Presidents and Pundits Keep Spinning Us to Death | Narrator |
| 2006 | All the King's Men (2006) | Willie Stark |
| 2005 | The Interpreter (2005) | Tobin Keller |
| 2004 | Pauly Shore Is Dead | Self |
| 2004 | The Assassination of Richard Nixon | Samuel Byck |
| 2003 | This So-Called Disaster | Himself / Ray |
| 2003 | Mystic River | Jimmy Markum |
| 2003 | 21 Grams | Paul Rivers |
| 2003 | It's All About Love | Marciello |
| 2002 | September 11 | Director, Writer |
| 2001 | The Pledge | Director, Producer |
| 2001 | I Am Sam | Sam Dawson |
| 2001 | Dogtown and Z-Boys | Narrator |
| 2001 | Weird Wednesday: The Beaver Trilogy | Groovin' Larry (segment Beaver Kid 2) |
| 2000 | Up At The Villa | Rowley Flint |
| 2000 | Before Night Falls | Cuco Sanchez |
| 2000 | The Weight of Water | Thomas |
| 1999 | Sweet and Lowdown | Emmet Ray |
| 1998 | Hurlyburly | Eddie |
| 1998 | The Thin Red Line | Sgt. Welsh |
| 1997 | The Game | Conrad Van Orton |
| 1997 | She's So Lovely | Eddie Quinn |
| 1997 | U - Turn | Bobby Cooper |
| 1995 | Dead Man Walking (1995) | Matthew Poncelet |
| 1995 | The Crossing Guard | Director, Producer, Writer |
| 1993 | Carlito's Way | David Kleinfeld |
| 1991 | The Indian Runner | Director, Producer, Writer |
| 1990 | State of Grace (1990) | Terry Noonan |
| 1989 | Casualties of War | Meserve |
| 1986 | At Close Range | Brad Whitewood Jr. |
| 1986 | Shanghai Surprise | Glendon Wasey |
| 1985 | The Falcon and the Snowman | Daulton Lee |
| 1984 | Racing With the Moon | Henry 'Hopper' Nash |
| 1983 | Bad Boys (1983) | Mick O'Brien |
| 1982 | Fast Times at Ridgemont High | Jeff Spicoli |
| 1981 | Taps | Cadet Captain Alex Dwyer |
