| Year | Title | Role | Notes |
| 1993 | The Positively True Adventures of the Alleged Texas Cheerleader-Murdering Mom | Police Officer | Television film |
| 1993–2000 | Late Night with Conan O'Brien | Himself (co-host) | 1,247 episodes; also writer |
| 1995 | Mr. Show with Bob and David | Himself | Episode: "The Cry of a Hungry Baby" |
| 1998 | Upright Citizens Brigade | Hansel | Episode: "Story of the Toad" |
| Saturday Night Live | Drinky Crow | Voice, episode: "Cameron Diaz/Smashing Pumpkins"; uncredited |
| 1999 | LateLine | Himself | Episode: "Pearce on Conan" |
| 2000 | Strangers with Candy | Various roles | 3 episodes |
| Just Shoot Me! | Alan | Episode: "Choosing to Be Super" |
| DAG | Himself | Episode: "Pilot"; uncredited |
| 2002 | Ed | Barney Sticuzo | Episode: "Youth Bandits" |
| Malcolm in the Middle | Dr. Kennedy | Episode: "Clip Show" |
| Primetime Glick | Himself | Episode: "Andy Richter / Alec Baldwin" |
| 2002–03 | Andy Richter Controls the Universe | Andy Richter | 19 episodes; also producer |
| 2003 | The Lyon's Den | Kelly Robbins | Episode: "Ex" |
| 2004 | Happy Family | Clerk | Episode: "The Headboard" |
| It's All Relative | Dr. Bob | Episode: "Philip in a China Shop" |
| Father of the Pride | Nelson | Episode: "What's Black, White and Depressed All Over?" |
| 2004–05 | Crank Yankers | Lloyd | Voice, 3 episodes |
| Quintuplets | Bob Chase | 22 episodes |
| 2005–06, 2013 | Arrested Development | The Richter Brothers | 9 episodes |
| 2005 | Will & Grace | Dale | Episode: "The Old Man and the Sea" |
| 2006–08 | The New Adventures of Old Christine | Stan | 4 episodes |
| 2006–12 | Metalocalypse | Various voices | 3 episodes |
| 2006–23 | American Dad! | 16 episodes |
| 2007 | The Naked Trucker and T-Bones Show | Mayor William Q. Lefawn | Episode: "Key to the City" |
| Andy Barker, P . | Andy Barker | 6 episodes; also producer |
| Clark and Michael | Jerry Lillard | Episode: "DA Dad and the Break-Up" |
| 30 Rock | Mitch Lemon | Episode: "Ludachristmas" |
| 2007–08 | Monk | Hal Tucker | 2 episodes |
| 2008 | The Sarah Silverman Program | Potential Adoptive Parent | Episode: "Fetus Don't Fail Me Now" |
| King of the Hill | Wesley Cherish | Voice, episode: "Straight as an Arrow" |
| 2008–11 | The Mighty B! | Benjamin Higgenbotton | Voice, 16 episodes |
| Robot Chicken | Various voices | 2 episodes |
| 2008–15 | The Penguins of Madagascar | Mort | Voice, 82 episodes |
| 2009 | Bones | Henry Simon | Episode: "Double Trouble in the Panhandle" |
| True Jackson, VP | Simon Christini | Episode: "The Rival" |
| Chuck | Brad | Episode: "Chuck Versus the Suburbs" |
| The Goode Family | Fred Ridley | Voice, episode: "Public Disturbance" |
| Merry Madagascar | Mort | Voice, television special |
| 2009–10 | The Tonight Show with Conan O'Brien | Himself (co-host) | 145 episodes; also writer and announcer |
| 2010 | The Suite Life on Deck | Brother Theodore | Episode: "The Silent Treatment" |
| Running Wilde | Dan Thorngood | Episode: "The Junior Affair" |
| Glory Daze | Priest | Episode: "Hungry Like Teen Wolf" |
| 2010–21 | Conan | Himself (co-host) | Also writer and announcer |
| 2011 | Jon Benjamin Has a Van | "Celebrity Parkour" competitor | Episode: "The Van Scheme" |
| 2011–15 | China, IL | Agent Green | Voice, 4 episodes |
| 2012 | Hot in Cleveland | Father Brian | Episode: "Claus, Tails & High-Pitched Males: Birthdates 3" |
| 2012–14 | Comedy Bang! Bang! | Himself / narrator | 3 episodes |
| 2013 | Happy Endings | Roy | Episode: "Bros Before Bros" |
