Filmography
| Year | Title | Role |
| 2023 | Air (2023) | Phil Knight |
| 2023 | Hypnotic (2023) | Daniel Rourke |
| 2023 | Kiss the Future (2024) | Producer |
| 2021 | The Last Duel (2021) | Count Pierre d'Alençon |
| 2021 | The Tender Bar (2021) | Uncle Charlie |
| 2021 | Zack Snyder's Justice League (2021) | Batman/Bruce Wayne |
| 2020 | The Way Back (2020) | Jack Cunningham |
| 2020 | The Last Thing He Wanted | Treat Morrison |
| 2019 | Triple Frontier | Tom "Redfly" Davis |
| 2019 | Jay & Silent Bob Reboot | Holden McNeil |
| 2017 | Justice League (2017) | Batman/Bruce Wayne |
| 2017 | Bending the Arc | Executive Producer |
| 2016 | Batman v Superman: Dawn of Justice | Bruce Wayne/Batman |
| 2016 | The Accountant | Christian Wolff |
| 2016 | Live by Night | Joe Coughlin |
| 2014 | Gone Girl | Nick Dunne |
| 2013 | Runner Runner | Ivan Block |
| 2012 | Argo | Tony Mendez |
| 2012 | To the Wonder | Neil |
| 2010 | The Town | Doug MacRay |
| 2010 | The Company Men | Bobby Walker |
| 2009 | He's Just Not That Into You | Neil |
| 2009 | State of Play | Stephen Collins |
| 2009 | Reporter | Executive Producer |
| 2009 | Extract | Dean |
| 2007 | Smokin' Aces | Jack Dupree |
| 2007 | Gone Baby Gone | Director, Writer |
| 2006 | Feast | Executive Producer |
| 2006 | Hollywoodland | George Reeves |
| 2006 | Clerks II | Gawking Guy |
| 2004 | Jersey Girl | Ollie Trinke |
| 2004 | Fahrenheit 9/11 | Self |
| 2004 | Surviving Christmas | Drew Latham |
| 2003 | Daredevil | Matt Murdock/Daredevil |
| 2003 | Gigli | Gigli |
| 2003 | The Battle of Shaker Heights | Executive Producer |
| 2003 | Paycheck | Michael Jennings |
| 2002 | Stolen Summer | Producer |
| 2002 | The Third Wheel | Michael |
| 2002 | Changing Lanes | Gavin Banek |
| 2002 | The Sum of All Fears | Jack Ryan |
| 2001 | Pearl Harbor | Rafe McCawley |
| 2001 | Jay and Silent Bob Strike Back | Holden/Ben/Chuckie |
| 2001 | Daddy and Them | Lawrence Bowen |
| 2000 | Reindeer Games | Rudy Duncan |
| 2000 | Boiler Room | Jim Young |
| 2000 | Bounce | Buddy Amaral |
| 2000 | Joseph: King of Dreams | Joseph |
| 1999 | Dogma | Bartleby/Barry |
| 1999 | Forces of Nature (1999) | Ben Holmes |
| 1999 | 200 Cigarettes | Bartender |
| 1998 | Shakespeare in Love | Ned Alleyn |
| 1998 | Armageddon | A.J. Frost |
| 1998 | Phantoms | Sheriff Bryce Hammond |
| 1997 | Chasing Amy | Holden McNeil |
| 1997 | Good Will Hunting | Chuckie Sullivan |
| 1997 | Going All the Way: The Director's Edit | Gunner Casselman |
| 1995 | Mallrats | Shannon Hamilton |
| 1993 | Dazed and Confused | Fred O'Bannion |
| 1992 | School Ties | Chesty Smith |
