* 1985: The Goonies as Francis Fratelli
* 1986: Back to School as Jason Melon
* 1987: Adventures in Babysitting as Daryl Coopersmith
* 1988: License to Drive as Dean Rusty Ryan
* 1989: Bill & Ted's Excellent Adventure as Theodore Logan
* 1990: Problem Child as Junior Healy
* 1990: Earth Girls Are Easy as Woody
* 1991: Point Break as Angelo Pappas
* 1991: Once Upon a Crime as Augustus "Augie" Morosco
* 1992: My Cousin Vinny as "Vinny Gambini"
* 1993: Son in Law as Crawl
* 1993: Much Ado About Nothing as Claudio
* 1994: Ace Ventura: Pet Detective as Ray Finkle
* 1994: Dumb and Dumber as Lloyd Christmas
* 1996: Cable Guy as Steven Kovacs
* 1996: Kingpin as Ishmael
* 1997: Liar Liar as Fletcher Reede
* 1998: There's Something About Mary as Ted Stroehmann
* 1998: Dr. Dolittle as Archie
* 2000: Me, Myself & Irene as Charlie Baileygates
* 2001: Shallow Hal as Hal Larson
* 2003: Bruce Almighty as Bruce Nolan
* 2005: Bewitched as Jack Wyatt
* 2007: I Now Pronounce You Chuck and Larry as Larry Valentine
* 2008: Yes Man as Carl Allen
* 2009: Fun with Dick and Jane as Dick Harper
* 2012: Ted as John Bennett
* 2012: The Three Stooges as Moe Howard
* 2014: Dumb and Dumber To as Lloyd Christmas
* 2018: Dog Days as Glenn Morris
* 2022: Superpower Dogs as Himself
Television
* 1984: Silver Spoons as Eddie Keaton (2 episodes)
* 1985: Benson as Timmy (1 episode)
* 1996: Saturday Night Live (host; Episode: "John Goodman/The Wallflowers")
* 2003: Saturday Night Live (host; Episode: "Ben Affleck/Christina Aguilera")
* 2005–2006: The Comeback as Michael Patrick King
* 2008: Entourage as Himself (Season 5, Episode 3)
* 2012: 30 Rock as Paul L'Astnamé (Season 7, Episode 13)
* 2013: Parks and Recreation as Eddie Carr (Season 5, Episode 14)
* 2014–2015: Maron as Himself (5 episodes)
* 2017: Young Sheldon as Mr. Lundy (Season 1, Episode 8)
* 2018: The Kominsky Method as Eddie Farrnkopf (9 episodes)