- Rendition (2007) …. Douglas Freeman
- Zodiac (2007/I) …. Robert Graysmith
- Jarhead (2005) …. Anthony Swofford
- Proof (2005) …. Hal
- Brokeback Mountain (2005) …. Jack Twist
- The Man Who Walked Between the Towers (2005) …. Narrator
- The Day After Tomorrow (2004) …. Sam Hall
- Moonlight Mile (2002) …. Joe Nast
- Highway (2002/I) …. Pilot Kelson
- The Good Girl (2002) …. Holden Worther
- Lovely & Amazing (2001) …. Jordan
- Bubble Boy (2001) …. Jimmy Livingston
- Donnie Darko (2001) …. Donnie Darko
- October Sky (1999) …. Homer Hickam
- Homegrown (1998) …. Jake/Blue Kahan
- Homicide: Life on the Street …. Matt Ellison (1 episode, 1994)
- Josh and S.A.M. (1993) …. Leon
- A Dangerous Woman (1993) (as Jacob Gyllenhaal) …. Edward
- City Slickers (1991) …. Danny Robbins
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