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| Year | Title | Role | Notes |
| --- | --- | --- | --- |
| 1979 | Working Stiffs | Heimlich | 2 episodes |
| 1980–1981 | The Flintstone Comedy Show | Freaky Frankenstone | Voice, 18 episodes (The Frankenstones segment) |
| 1980 | Steve Martin: Comedy Is Not Pretty | Various roles | Television special |
| 1980 | Steve Martin: All Commercials | Various roles | Television special |
| 1981 | Mork & Mindy | Dickie Nimitz | Episode: "Long Before We Met" |
| 1981 | The Pee-wee Herman Show | Pee-wee Herman | Television special |
| 1982 | Madame's Place | Himself | Season: 1 Episode: 34 |
| 1984 | Faerie Tale Theatre | Pinocchio | Season: 3 Episode: 3 "Pinocchio" |
| 1984 | Cheeseball Presents | Pee-wee Herman | TV movie |
| 1985 | Saturday Night Live | Pee-wee Herman (host) | Episode: "Pee-wee Herman/Queen Ida & The Bon Temps Zydeco Band" |
| 1986–1990 | Pee-wee's Playhouse | Pee-wee Herman | 45 episodes; also creator, writer, director, executive producer and set decorator Daytime Emmy Award for Outstanding Achievement in Art Direction/Set Direction/Scenic Design (1988) Daytime Emmy Award for Outstanding Achievement in Graphics and Title Design (1991) Nominated – Daytime Emmy Award for Outstanding Performer in Children's Programming (1987–1988, 1990–1991) Nominated – Daytime Emmy Award for Outstanding Children's Series (1987, 1990–1991) Nominated – Daytime Emmy Award for Outstanding Writing For A Children's Series (1987–1988) Nominated – Daytime Emmy Award for Outstanding Directing For A Children's Series (1988, 1990–1991) Nominated – Daytime Emmy Award for Outstanding Achievement in Art Direction/Set Decoration/Scenic Design (1989–1991) |
| 1987 | 227 | Pee-wee Herman | Episode: "Toyland" |
| 1988 | Sesame Street | Pee-wee Herman | Episode: "Put Down the Duckie" |
| 1988 | Pee-wee's Playhouse Christmas Special | Pee-wee Herman | Television special; also writer, director and executive producer |
| 1995–1997 | Murphy Brown | Andrew J. Lansing III | 6 episodes Nominated – Primetime Emmy Award for Outstanding Guest Actor in a Comedy Series (1995) |
| 2000 | Everybody Loves Raymond | Russell | Episode: "Hackidu" |
| 2001 | You Don't Know Jack | Troy Stevens | 6 episodes |
| 2001 | Ally McBeal | Louis | Episode: "Cloudy Skies, Chance of Parade" |
| 2002 | Rugrats | Hermie the Elf | Voice, episode: "Babies in Toyland" |
| 2002 | The Groovenians | Jet | Voice; pilot |
| 2005 | Tripping the Rift | God / Devil | Voice, episode: "Chode's Near Death-Experience" |
| 2006 | Campus Ladies | Drama instructor | Episode: "Drama Class" |
| 2006 | Reno 911! | Rick | Episode: "Rick's On It" |
| 2006 | Re-Animated | Golly Gopher | Voice, television film |
| 2007 | Area 57 | Alien | Pilot |
| 2007 | 30 Rock | Gerhardt Hapsburg | Episode: "Black Tie" |
| 2007 | Dirt | Chuck Lafoon | 3 episodes |
| 2007 | Tim and Eric Awesome Show, Great Job! | The Moon | Episode: "Cats" |
| 2007 | Pushing Daisies | Oscar Vibenius | 2 episodes |
| 2007–2009 | Chowder | Reuben | Voice, 3 episodes |
| 2009–2011 | Batman: The Brave and the Bold | Bat-Mite | Voice, 4 episodes |
| 2010 | Adventure Time | Gnome Ruler | Voice, episode: "Power Animal" |
| 2010 | WWE Raw | Pee-wee Herman | 1 episode; special guest |
| 2011 | The Pee-wee Herman Show on Broadway | Pee-wee Herman | Television special Nominated – Primetime Emmy Award for Outstanding Variety, Music, or Comedy Special |
| 2012–2013 | Tron: Uprising | Pavel | Voice, 17 episodes |
| 2012–2015 | Robot Chicken | The Riddler / Sunbather | Voice, 3 episodes |
| 2013 | Comedy Bang! Bang! | Pee-wee Herman | Episode: "Pee Wee Herman Wears a Halloween Costume" |
| 2014 | Teenage Mutant Ninja Turtles | Martin Milton/Sir Malachi | Voice, episode: "Mazes and Mutants" |
| 2014 | Sanjay and Craig | Benji Warlin | Voice, episode: "Googas" |
| 2014 | Star Wars Rebels | RX-24 | Voice, episode: "Droids in Distress" |
| 2014 | Lego DC Comics: Batman Be-Leaguered | Bat-Mite | Voice, television film |
| 2014 | Phineas and Ferb | Professor Parenthesis | Voice, episode: "The O.W.C.A. Files" |
| 2014 & 2016 | American Dad! | Wyatt Borden | Voice, episode: "Blagsnarst, a Love Story" |
| 2014–2015 | The Blacklist | Mr. Vargas | 5 episodes |
| 2015 | Portlandia | Weirdos' Lawyer | Episode: "Dead Pets" |
| 2015–2016 | Pickle and Peanut | Couch Dracula | Voice, 2 episodes |
| 2015–2017 | Penn Zero: Part-Time Hero | The Milk Man/The Butterman | Voice, 3 episodes |
| 2016–2017 | Gotham | Elijah Van Dahl | 3 episodes |
| 2017–2018 | Voltron: Legendary Defender | Unliu Swap Shop Owner | Voice, 3 episodes |
| 2018 | Mosaic | JC Schiffer | 7 episodes |
| 2018–2019 | Legends of Tomorrow | Dybbuk | Voice, 5 episodes |
| 2019 | Tigtone | Cryptomb | Voice, episode: "Tigtone and the Cemetery of the Dead" |
| 2019 | What We Do in the Shadows | Paul | Episode: "The Trial" |
| 2019 | The Conners | Sandy Bitensky | Episode: "Lanford, Toilet of Sin" |
| 2021 | The Tom and Jerry Show | Pontius Pig | Voice, episode: "Sock It to Me" |
| 2023 | Bob's Burgers | Pat | Voice, episode: "Amelia" (Final role; dedicated in memory) |