| Movie | 1980 | The Blues Brothers | Waiter | |
| Movie | 1992 | Buffy the Vampire Slayer | Amilyn | |
| Movie | 1986 | Flight of the Navigator | Max (voice) | |
| Movie | 2001 | Blow | Derek Foreal | |
| Movie | 1996 | Matilda | FBI Agent | |
| Movie | 1981 | Nice Dreams | Howie Hamburger Dude | |
| Movie | 1981 | The Pee-wee Herman Show | Pee-wee Herman | |
| Movie | 2011 | WWE WrestleMania XXVII | Pee-wee Herman (Appearance) | |
| Movie | 1985 | Pee-wee's Big Adventure | Pee-wee Herman | |
| Movie | 1988 | Big Top Pee-wee | Pee-wee Herman | |
| Movie | 1968 | The Brotherhood | Wedding Guest (uncredited) | |
| Movie | 2000 | South of Heaven, West of Hell | Arvid Henry | |
| Movie | 1980 | Pray TV | Jack Chudnowski | |
| Movie | 1993 | The Nightmare Before Christmas | Lock (voice) | |
| Movie | 1999 | Mystery Men | Spleen | |
| Movie | 1997 | Beauty and the Beast: The Enchanted Christmas | Fife (voice) | |
| Movie | 1980 | Cheech & Chong's Next Movie | Pee Wee Herman / Desk Clerk (Groundling) | |
| Movie | 2011 | The Smurfs | Jokey Smurf (voice) | |
| Movie | 2011 | The Pee-wee Herman Show on Broadway | Pee-wee Herman | |
| Movie | 1997 | Buddy | Professor Spatz | |
| Movie | 1996 | Dunston Checks In | Buck LaFarge | |
| Movie | 2010 | Life During Wartime | Andy Kornbluth | |
| Movie | 1982 | Lily for President? | Pee Wee Herman | |
| Movie | 1982 | Pandemonium | Johnson | |
| Movie | 1978 | School, Girls, and You! | Wally Bile | |
| Movie | 1982 | Twilight Theatre | Pee Wee Herman | |
| Movie | 2013 | The Final Moments of Karl Brant | Bennett Ferryman | |
| Movie | 2013 | Tom and Jerry's Giant Adventure | Screwy Squirrel (voice) | |
| Movie | 2015 | O.W.C.A. Files | Parenthesis (voice) | |
| Movie | 2013 | Tales from the Warner Bros. Lot | Self | |
| Movie | 1981 | Dream on! | | |
| Movie | 2010 | Gavin McInnes is a Fucking Asshole | Pee-Wee Herman (archive footage) | |
| Movie | 2023 | Quiz Lady | Francine's Crush | |
| Movie | 1988 | Moonwalker | Pee-wee Herman (voice) (uncredited) | |
| Movie | 1987 | Back to the Beach | Pee-Wee Herman | |
| Movie | 2013 | Scooby-Doo! Mecha Mutt Menace | Irv (voice) | |
| Movie | 2024 | The World According to Allee Willis | Self (archive footage) | |
| Movie | 1988 | Pee-wee's Playhouse Christmas Special | Pee-wee Herman | |
| Movie | 1980 | Midnight Madness | Pinball City Proprietor | |
| Movie | 2015 | Accidental Love | Edwin | |
| Movie | 1987 | The Thrill Can Kill | Pee-Wee Herman | |
| Movie | 1980 | Steve Martin: Comedy Is Not Pretty | Cafe Counter Guy | |
| Movie | 1984 | Meatballs: Part II | Albert | |
| Movie | 2015 | Above and Beyond | Self | |
| Movie | 2004 | Teacher's Pet | Dennis (voice) | |
| Movie | 2012 | Robot Chicken: DC Comics Special | The Riddler (voice) | |
| Movie | 2015 | Robot Chicken DC Comics Special III: Magical Friendship | The Riddler (voice) | |
| Movie | 2014 | Robot Chicken DC Comics Special II: Villains in Paradise | The Riddler / Sunbather (voice) | |
| Movie | 2014 | LEGO DC Comics Super Heroes: Batman Be-Leaguered | Bat-Mite (voice) | |
| Movie | 2007 | Reno 911!: Miami | Sir Terrence | |
| Movie | 2021 | Crack: Cocaine, Corruption & Conspiracy | Self (archive footage) | |
| Movie | 2012 | Beauty Is Embarrassing | Self | |
| Movie | 2006 | Re-Animated | Golly Gopher (voice) | |
| Movie | N/A | Twilight Park | Carny/Mime | |
| Movie | 1984 | Pinocchio | Pinocchio | |
| Movie | 2013 | The Smurfs 2 | Jokey Smurf (voice) | |
| Movie | 2003 | Overnight | Self | |
| Movie | 2016 | Gigglefudge USA! | Self | |
| Movie | 2007 | Area 57 | The Alien | |
| Movie | 1992 | Batman Returns | Penguin's Father | |
| Movie | 2002 | Rugrats: Babies in Toyland | Hermie the Elf (voice) | |
| Movie | 1980 | All Commercials... A Steve Martin Special | Self | |
| Movie | 1984 | Cheeseball Presents | | |
| Movie | 2006 | The Tripper | Frank Baker | |
| Movie | 1983 | Likely Stories Vol. 2 | | |
| Movie | 2003 | Mayor of the Sunset Strip | Self | |
| Movie | 1998 | Doctor Dolittle | Raccoon (voice) | |
| Movie | 1983 | The Paragon of Comedy | Arnie / Pee-wee Herman | |
| Movie | 2016 | Pee-wee's Big Holiday | Pee-wee Herman | |
| Movie | 1988 | Sesame Street: Put Down the Duckie | Pee-wee Herman | |
| Movie | 2021 | The Crown with a Shadow | Oliver (voice) | |
| Movie | 2002 | The Groovenians | Jet/The Bubbie | |
| Movie | 1985 | All-Star Rock 'N' Wrestling Saturday Spectacular | Pee-Wee Herman | |
| Movie | 1990 | Sesame Street: Sing Yourself Silly! | Pee-Wee Herman (archive footage) | |
| Movie | 1984 | Cheeseball Presents | Pee-Wee Herman | |
| Movie | 1975 | A Comedy in Six Unnatural Acts | | |
| Movie | 2003 | 101 Most Shocking Moments in Entertainment | Self (archive footage) | |
| Movie | 2024 | DEVO | Pee-wee Herman (archive footage) | |
| TV Show | 2007 | Dirt | Chuck Lafoon | 3 |
| TV Show | 2004 | Best Week Ever | | 1 |
| TV Show | 1997 | Ally McBeal | Louis | 1 |
| TV Show | 2003 | Jimmy Kimmel Live! | Self | 4 |
| TV Show | 1996 | Everybody Loves Raymond | Russell | 1 |
| TV Show | 1985 | 227 | Pee-Wee Herman | 1 |
| TV Show | 2003 | Reno 911! | Rick | 1 |
| TV Show | 1992 | The Tonight Show with Jay Leno | | 1 |
| TV Show | 1996 | E! True Hollywood Story | Self | 1 |
| TV Show | 1978 | Mork & Mindy | Dickie Nimitz | 1 |
| TV Show | 2006 | Campus Ladies | | 1 |
| TV Show | 1982 | Faerie Tale Theatre | Pinocchio | 1 |
| TV Show | 2006 | 30 Rock | Gerhardt | 1 |
| TV Show | 1986 | Pee-wee's Playhouse | Pee-wee Herman | 45 |
| TV Show | 2020 | The Holiday Movies That Made Us | Self (archive footage) | 1 |
| TV Show | 2007 | Pushing Daisies | Oscar Vibenius | 2 |
| TV Show | 2009 | The Jay Leno Show | Self | 1 |
| TV Show | 1993 | Late Night with Conan O'Brien | Self - Guest | 1 |
| TV Show | 2001 | You Don't Know Jack | Troy Stevens | 6 |
| TV Show | 1979 | Working Stiffs | | 1 |
| TV Show | 2010 | Adventure Time | Gnome Ruler/Dancing Bug (voice) | 1 |
| TV Show | 2005 | Hopeless Pictures | | 8 |
| TV Show | 1984 | MTV Video Music Awards | Pee-wee Herman | 1 |
| TV Show | 2012 | TRON: Uprising | Pavel | 18 |
| TV Show | 1975 | Saturday Night Live | Pee-Wee Herman - Host | 1 |
| TV Show | 1975 | Saturday Night Live | Self - Cameo (uncredited) | 1 |
| TV Show | 2011 | Portlandia | Weirdos' Lawyer | 1 |
| TV Show | 2012 | Comedy Bang! Bang! | Pee-Wee Herman | 1 |
| TV Show | 2011 | Bob's Burgers | Pat (voice) | 1 |
| TV Show | 2005 | American Dad! | | 1 |
| TV Show | 2013 | The Blacklist | Mr. Vargas | 5 |
| TV Show | 2018 | Minecraft: Story Mode | Ivor (voice) | 5 |
| TV Show | 2007 | Chowder | Reuben (voice) | 2 |
| TV Show | 1962 | The Tonight Show Starring Johnny Carson | Self | 5 |
| TV Show | 1988 | Murphy Brown | Andrew J. Lansing III | 6 |
| TV Show | 2014 | Penn Zero: Part-Time Hero | The Butterman (voice) | 1 |
| TV Show | 2014 | Penn Zero: Part-Time Hero | The Milkman (voice) | 2 |
| TV Show | 2007 | Tim and Eric Awesome Show, Great Job! | The Moon | 1 |
| TV Show | 2018 | Mosaic | JC Schiffer | 6 |
| TV Show | 2004 | Tom Goes to the Mayor | Paul (voice) | 1 |
| TV Show | 1982 | Faerie Tale Theatre | Guest Interviewee | 1 |
| TV Show | 2014 | Gotham | Elijah Van Dahl | 3 |
| TV Show | 2002 | The Groovenians | Jet / The Bubble (voice) | 1 |
| TV Show | 2014 | The Tonight Show Starring Jimmy Fallon | Self | 2 |
| TV Show | 2014 | Star Wars Rebels | RX-24 (voice) | 1 |
| TV Show | 2016 | DC's Legends of Tomorrow | Dybbuk (voice) | 5 |
| TV Show | 2019 | What We Do in the Shadows | Paul | 1 |
| TV Show | 2018 | The Conners | Sandy Bitensky | 1 |
| TV Show | 2016 | To Tell the Truth | Self - Disguised Contestant | 3 |
| TV Show | 2016 | To Tell the Truth | Self - Panelist | 1 |
| TV Show | 2005 | American Dad! | Wyatt Borden (voice) | 1 |
| TV Show | 1982 | Madame's Place | Pee Wee Herman | 1 |
| TV Show | 1980 | The Flintstone Comedy Show | Freaky Frankenstone | 126 |
| TV Show | 2021 | Celebrity Wheel of Fortune | Self - Contestant | 1 |
| TV Show | 1980 | The Frankenstones | Freaky Frankenstone (voice) | 11 |
| TV Show | 2008 | Batman: The Brave and the Bold | Bat-Mite (voice) | 4 |
| TV Show | 2010 | Conan | Self | 2 |
| TV Show | 2025 | Pee-wee as Himself | Self | 2 |
| TV Show | 1987 | Dolly | Pee-wee Herman | 1 |
| TV Show | 1944 | Golden Globe Awards | Pee-wee Herman - Presenter | 1 |