| Year | Title | Role | Notes |
| 1994 | Understanding | Quark | Episode: "Uncertainty" |
| 1995–1999;2002 | Dr. Katz, Professional Therapist | Ben, Various voices | 80 episodesAlso writer |
| 1997 | The Chris Rock Show | Extra | 1 episode |
| The Jenny McCarthy Show | Various | 6 episodes |
| 1997–2000 | Science Court | Prof. Nick Parsons (voice) | 29 episodes |
| 1998 | Sex and the City | Jeff | Episode: "Bay of Married Pigs" |
| Upright Citizens Brigade | Various | 10 episodes |
| 1999 | Dick and Paula Celebrity Special | Various | 2 episodesAlso writer |
| Space Ghost Coast to Coast | Himself | Episode: "King Dead" |
| 1999–2004 | Home Movies | Coach John McGuirk, Jason Penopolis, Various voices | 52 episodesAlso writer and producer |
| 2001–2009 | Aqua Teen Hunger Force | Various voices | 5 episodes |
| 2002 | Saddle Rash | Gummy, Tommy Morgan (voices) | PilotAlso writer |
| 2003 | Hey Monie! | Self-defense instructor | 1 episode |
| 2004 | Pilot Season | Ken Fold | 2 episodes |
| Say Uncle | Jonny | Failed pilot |
| 2004–2006 | Cheap Seats: Without Ron Parker | Rabbi Marc Shalowitz, Gene Stapleton | 4 episodes |
| O'Grady | Kevin Harnisch, Iris, Philip (voices) | 19 episodes |
| 2005 | Rescue Me | Gary | Episode: "Rebirth" |
| 2005–2006 | Sunday Pants | Bob the Log | Travel Logs shorts |
| 2005–2007 | Lucy, the Daughter of the Devil | Satan, Special Father (voices) | 11 episodesAlso writer |
| 2006 | Freak Show | Tuck, Various voices | 7 episodesAlso co-creator, writer and executive producer |
| 2006–2008 | Assy McGee | The Mayor, Various voices | 19 episodesAlso writer and consulting producer |
| 2006–2012 | The Venture Bros. | The Master (voice) | 4 episodes |
| 2006–present | Family Guy | Carl Graves, Bob Belcher, Various voices | 27 episodes |
| 2007–2008 | Human Giant | Various | 4 episodesAlso consultant writer |
| 2007–2015 | WordGirl | Reginald the Jewelry Store Clerk, InvisiBill, Additional Voices | 31 episodes |
| 2009 | Michael & Michael Have Issues | Larry | Episode: "Frog Box" |
| Paid Programming | Various | PilotCo-creator, writer and executive producer |
| Parks and Recreation | Scott Braddock | Episode: "Kaboom" |
| Titan Maximum | Tap Banister (voice) | Episode: "Dirty Lansbury" |
| 2009–2010 | Important Things with Demetri Martin | Various | 7 episodesAlso writer and co-producer |
| 2009–2023 | Archer | Sterling Archer (voice) | 145 episodes |
| 2011 | Jon Benjamin Has a Van | Host | 10 episodesAlso co-creator, writer and executive producer |
| Soul Quest Overdrive | Mortimer (voice) | 6 episodesAlso co-creator and co-writer |
| American Dad! | Talking Cabbage (voice) | Episode: "License to Till" |
| 2011–present | Bob's Burgers | Bob Belcher, Jimmy Pesto Jr., Various voices | Main role |
| 2012 | Suburgatory | Tabitha | Episode: "Ryan's Song" |
| Ugly Americans | Dick Maggotbone (voice) | Episode: "Mark Loves Dick" |
| 2013 | Nathan for You | Himself | Episode: "Yogurt Shop/Pizzeria" |
| 2014–2025 | Last Week Tonight with John Oliver | Ben, Scientist, Defendant, Blank Void, Air Traffic Controller | 6 episodes |
| 2015 | Conan | Sterling Archer (voice) | Episode: "677" |
| Wet Hot American Summer: First Day of Camp | Can of Vegetables, Mitch | 4 episodes |
| The Jim Gaffigan Show | Kevin | Episode: "The Bible Story" |
| The Adventures of Puss in Boots | Baltasar (voice) | Episode: "Luck" |
| All Hail King Julien | Fred (voice) | 5 episodes |
| 2015–2017 | Master of None | Benjamin | 4 episodes |
| 2016–2017 | People of Earth | Officer Glimmer | 8 episodes |
| 2017 | Wet Hot American Summer: Ten Years Later | Can of Vegetables, Mitch | 5 episodes |
| Difficult People | Brian | Episode: "Fuzz Buddies" |
