| Year | Title | Role | Notes |
|---|
| 1987–1991 | Saturday Night Live | Various roles | 13 episodes; also writer |
| 1991–1992 | Get a Life | — | Writer |
| 1992 | The Dennis Miller Show | — |
| The Ben Stiller Show | Various roles | 13 episodes; also writer |
| 1993 | The Jackie Thomas Show | Elmer | Episode: "Aloha, Io-wahu" |
| Roseanne | Jim | Episode: "Tooth or Consequences" |
| 1993–1998 | The Larry Sanders Show | Steve Grant | 11 episodes |
| 1993–1994 | Late Night with Conan O'Brien | — | Writer |
| 1994 | Tom | David | Episode: "The Bad Seed" |
| Life on Mars | Bob | Pilot; also creator and writer |
| 1995–1998 | Mr. Show with Bob and David | Various roles | 30 episodes; also co-creator, writer and executive producer |
| 1996 | Dr. Katz, Professional Therapist | Bob | Voice; episode: "Fructose" |
| Seinfeld | Ben | Episode: "The Abstinence" |
| The Dana Carvey Show | — | Writer |
| 1997–1998 | NewsRadio | Dr. Smith / Bob | 2 episodes |
| 1997, 2001 | Everybody Loves Raymond | Scott Preman |
| 1997–2000 | Tenacious D | — | Co-creator, writer and executive producer |
| 1997 | Space Ghost Coast to Coast | Himself | Episode: "Gallagher" |
| 1999 | Just Shoot Me! | Barry | Episode: "The Odd Couple: Part 1" |
| 3rd Rock from the Sun | Gary Parkinson | Episode: "The Fifth Solomon" |
| 2000 | Curb Your Enthusiasm | Gil | Episode: "Porno Gil" |
| The Near Future | — | Pilot; co-creator, director, writer and executive producer |
| 2001 | Ed | Rev. Richie Porter | Episode: "Valentine's Day" |
| The Andy Dick Show | Chuck Charles | Episode: "Standards and Practices" |
| 2002 | Next! | Various roles | Pilot; also co-creator, writer and executive producer |
| 2003 | Highway to Oblivion | — | Pilot; director |
| Less than Perfect | Colin Hunter | Episode: "The New Guy" |
| Futurama | Chaz | Voice; episode: "The Why of Fry" |
| The Big Wide World of Carl Laemke | Carl Laemke | Pilot; also creator, writer and executive producer |
| Slice o' Life | (Role unknown) | Pilot |
| Arrested Development | Dr. Phil Gunty | Episode: "Visiting Ours" |
| 2004 | Joey | Brian Michael David Scott | Episode: "Joey and the Nemesis" |
| Aqua Teen Hunger Force | Bean Wizard | Voice; episode: "Hypno-Germ" |
| 2004–2006 | Tom Goes to the Mayor | Various roles | 21 episodes; also writer and executive producer |
| 2005 | Crank Yankers | Droopy | Voice; episode: "#3.14" |
| 2006 | Freak Show | Half Oldman Half Youngman / Senator Tinkerbell | Voice; 2 episodes |
| 2007–2010 | Tim and Eric Awesome Show, Great Job! | Various roles | 25 episodes; also creative consultant |
| 2007 | The Sarah Silverman Program | Mister Wadsworth | Episode: "Maid to Border" |
| Derek and Simon: The Show | Vance Hammersly | 3 episodes; also co-creator, writer, director and executive producer |
| 2008–2012 | How I Met Your Mother | Arthur Hobbs | 8 episodes |
| 2008 | Weeds | Barry | Episode: "Head Cheese" |
| Mike Birbiglia's Secret Public Journal | Donnie | Television special |
| David's Situation | — | Pilot; co-creator, director, writer and executive producer |
| 2009–2013 | Breaking Bad | Saul Goodman | 36 episodes |
| 2009 | American Dad! | Third Worker / TV Host | Voice; 2 episodes |
| The Goode Family | Brian Kennedy | Voice; episode: "Pleatherheads" |
| Glenn Martin, DDS | Vince the Circus Owner | Voice; episode: "The Grossest Show on Earth" |
| Rules of Engagement | Mike | Episode: "Russell's Secret" |
| 2010 | The Life & Times of Tim | The Interventionist / Bathroom Attendant | Voice; 2 episodes |
| Check It Out! with Dr. Steve Brule | — | Creative consultant |
| Entourage | Ken Austin | 3 episodes |
| Team Spitz | Principal Kersey | Pilot |
| Funny or Die Presents | Scott & Behr | Episode: "112" |
| 2011 | Let's Do This! | Cal | Pilot; also creator, director, writer and executive producer |
| Jon Benjamin Has a Van | Rev. Rocco Janson | Episode: "Smoking" |
| 2012 | NTSF:SD:SUV:: | Aaron Sampson | Episode: "Robot Town" |
| Bob's Burgers | Chase | Voice; episode: "Tina-rannosaurus Wrecks" |
| The League | Miles Miller | Episode: "A Krampus Carol" |
| 2012–2016 | Comedy Bang! Bang! | Various roles | 6 episodes |
| 2013 | The Office | Mark Franks | Episode: "Moving On" |
| 2013–2018 | Drunk History | Various roles | 4 episodes |
| 2013 | Ghost Ghirls | Frank van Stetten | Episode: "Ghost Writer" |
| Late Night with Jimmy Fallon | Saul Goodman | Episode: "5.191" |
| 2013–2014 | The Birthday Boys | Various roles | 11 episodes; also director, writer and executive producer |
| 2014 | Fargo | Chief Bill Oswalt | 9 episodes |
| TripTank | Hot Sauce Worker | Voice; episode: "Crossing the Line" |
| Tim & Eric's Bedtime Stories | Dr. Stork | Episode: "Toes" |
| 2015–2022 | Better Call Saul | Jimmy McGill | 63 episodes; also producer |
| 2015 | W/ Bob & David | Various roles | 4 episodes; also co-creator, writer and executive producer |
| 2017 | Nobodies | Himself | Episode: "Not the Emmys" |
| 2017–2018, 2021 | No Activity | Greg | 5 episodes |
| 2019–2022 | Undone | Jacob Winograd | 16 episodes; also producer |
| 2019 | The Simpsons [5] | Mob Lawyer | Voice; episode: "The Fat Blue Line" |
| The Kominsky Method | Dr. Shenckman | Episode: "Chapter 13. A Shenckman Equivocates" |
| 2020 | Corporate | Black Dog | Voice; episode: "Black Dog" |
| 2021 | Mom | Hank | Episode: "Tiny Dancer and an Impromptu Picnic" |
| I Think You Should Leave with Tim Robinson | Man in Diner | Episode: "They have a cake shop there Susan where the cakes just look stunning." |
| 2021–2022 | Chicago Party Aunt | Feather | Voice; 12 episodes |
| 2023 | Lucky Hank | William Henry "Hank" Devereaux, Jr. | 8 episodes; also executive producer |
| 2023, 2025 | The Bear | Uncle Lee | 2 episodes |
