| Year | Title | Role | Notes |
| 1992–1993 | The Ben Stiller Show | Stage Manager / Boyfriend | 2 episodesAlso writerPrimetime Emmy Award for Outstanding Writing for a Variety, Music or Comedy Program (1993) |
| 1995 | A Bucket of Blood | Charlie | Television film |
| 1995–1998 | Mr. Show with Bob and David | Various roles | 30 episodesAlso co-creator, writer and executive producerPrimetime Emmy Award for Outstanding Writing for a Variety, Music or Comedy Program (1998–1999)Nominated –Primetime Emmy Award for Outstanding Music and Lyrics (1998) |
| 1996–1997 | The Drew Carey Show | Earl | 2 episodes |
| 1996–1998 | NewsRadio | David / Theo | 2 episodes |
| 1997–1998 | Dr. Katz, Professional Therapist | David (voice) | 2 episodes |
| 1997–2000 | Tenacious D | Comic Dressed as Nun | Episode: "Angel in Disguise"Also co-creator, writer and executive producer |
| 1997 | Space Ghost Coast to Coast | Himself | Episode: "Gallagher" |
| 1998 | Hercules | Fear (voice) | Episode: "Hercules and the Owl of Athens" |
| 1999–2003 | Just Shoot Me! | Donnie DiMauro | 3 episodes |
| 2000 | Strangers with Candy | Dr. Trepanning | Episode: "Is My Daddy Crazy?" |
| 2001 | Night of the Living Doo | Himself (voice) | Television film |
| Home Movies | Guy in Grocery Store (voice) | Episode: "Brendon's Choice" |
| 2002–2008 | Aqua Teen Hunger Force | Happy Time Harry / Bert Banana (voices) | 3 episodes |
| 2002 | Never Mind the Buzzcocks | Himself | American version, panel game show, 1 episode |
| 2003–2004 | Oliver Beene | Future Oliver David Beene (voice) | 23 episodes |
| 2003 | King of the Hill | Ward Rackley (voice) | Episode: "Witches of East Arlen" |
| 2003–2004 | Crank Yankers | Benjamin Dubois / Ray Shanty (voices) | 2 episodes |
| 2003–2006,2013, 2018–2019 | Arrested Development | Dr. Tobias Fünke | 78 episodesNominated–Screen Actors Guild Award for Outstanding Performance by an Ensemble in a Comedy Series (2005–2006, 2014)Nominated–Satellite Award for Best Supporting Actor – Television Series (2004) |
| 2004 | Pilot Season | Ben (voice) | 2 episodes |
| 2005 | Tom Goes to the Mayor | Todd (voice) | Episode: "Calcucorn" |
| 2005–2007 | The Colbert Report | Russ Lieber | 7 episodes |
| 2006 | O'Grady | Randy Harnisch (voice) | Episode: "Big Jerk on Campus" |
| Wonder Showzen | T-Totaled Timbo / Junkyard Jessip / Storytime Hostage | 3 episodes |
| Freak Show | Benny / Primi / Various voices | 7 episodesAlso co-creator, writer, and executive producer |
| Family Guy | Jerry Kirkwood (voice) | Episode: "Prick Up Your Ears" |
| 2007–2008 | Tim and Eric Awesome Show, Great Job! | Pizza Boy / James the Pussy Doodles Artist / Lou | 3 episodes |
| 2007 | Law & Order: Criminal Intent | Ronnie Chase | Episode: "Bombshell" |
| Odd Job Jack | Julius J (voice) | Episode: "King Ho" |
| 2008 | David's Situation | David | PilotAlso co-creator and writer |
| Human Giant | Peter Burns | 2 episodes |
| 2009 | Important Things with Demetri Martin | Co-worker | Episode: "Chairs" |
| Paid Programming | | PilotAlso co-creator |
| 2010 | Kung Fu Panda Holiday | Crane | Voice |
| 2010–2011 | Running Wilde | Dr. Andy Weeks | 7 episodes |
| 2010–2012,2016 | The Increasingly Poor Decisions of Todd Margaret | Todd Margaret | 19 episodesAlso creator, writer, and associate and executive producer |
| 2011, 2018 | Archer | Noah (voice) | 6 episodes |
| 2011 | Soul Quest Overdrive | Bert (voice) | 6 episodes |
| 2011–2012 | Modern Family | Duane Bailey | 3 episodes |
| 2012 | Mary Shelley's Frankenhole | Jim Belushi / John Belushi (voices) | Episode: "Robert Louis Stevenson's Belushi" |
| 2012–2013 | Comedy Bang! Bang! | Himself / Chef | 2 episodes |
| 2013–2014 | The Heart, She Holler | Jack | 12 episodes |
| 2014 | Rick and Morty | Prince Nebulon (voice) | Episode: "M. Night Shaym-Aliens!" |
| Community | Hank Hickey | Episode: "Advanced Advanced Dungeons & Dragons" |
| Dead Boss | Derek Bridges | Pilot |
| Maron | Himself | Episode: "Marc's Family" |
| Drunk History | Baron von Steuben | Episode: "Philadelphia" |
| 2015 | Asylum | Juan Pablo | Episode: "Project Siren" |
| TripTank | Jack (voice) | Episode: "Precipice of Yesterday" |
