O'Brien was born in Brookline, Massachusetts to Irish-American parents. He attended Harvard University, where he was president of the "Harvard Lampoon", a humor magazine, twice. O'Brien moved to Los Angeles upon graduation to join the writing staff of HBO's Not Necessarily the News. He spent two years with that show, and performed regularly with several improvisational groups such as The Groundlings.
In January 1988 Saturday Night Live's executive producer Lorne Michaels hired O'Brien as a writer. Over his three-and-a-half years on SNL he wrote such recurring sketches as "Mr. Short-Term Memory" and "The Girl Watchers" (first performed by Tom Hanks and Jon Lovitz), and appeared as an extra in some skits. In 1989 he was awarded an Emmy Award for Outstanding Writing in a Comedy or Variety Series.
In the spring of 1991 O'Brien left SNL to write and produce a pilot for the TV show Lookwell, starring Adam West. It was broadcast on NBC in July but was not picked up as a series. That fall O'Brien signed on as a writer and producer for the Fox series The Simpsons, where he later became the supervising producer. His favorite episode, of the ones that he wrote, is "Marge vs. the Monorail."
On April 26, 1993, Conan was selected as the new host of Late Night with Conan O'Brien by Michaels. O'Brien and the Late Night writing team have consistently been nominated for an Emmy Award for Best Writing in a Comedy or Variety Series since 1996. In 1997 and 2000 he and the Late Night writing staff won the Writer's Guild Award for Best Writing in a Comedy/Variety Series.
In addition, O'Brien currently heads up Conaco, a production partnership with the network to develop programming for NBC primetime and other dayparts. Its first venture, the reality show Lost which debuted in fall of 2001.