Flaherty was born Joseph O'Flaherty Joe Flaherty Biography (1941-) in Pittsburgh, Pennsylvania, but moved to Chicago where he started his comedy career with the Second City Theater as Joe O'Flaherty. After seven years in Chicago, he moved to Toronto to help establish the Toronto Second City theatre troupe. During those years, he was one of the original writer/performers on SCTV, where he spent eight years on the show, playing such characters as Big Jim McBob (of Farm Film Report fame), Count Floyd/Floyd Robertson, and station owner/manager Guy Caballero who goes around in a wheelchair simply for the respect therein.

Other memorable Flaherty characterizations included emotional talk show host Sammy Maudlin, seedy saxophonist-private eye Vic Arpeggio, aggressive elocution lecturer Norman Gorman, myopic public television host Hugh Betcha and "crazy as a snake" ex-convict Rocco.

SCTV ceased production in 1984.

Throughout his film career, Flaherty has appeared in a number of cult favorites, for example, playing the part of the Western Union postal worker who delivers Doc Brown's 70-year-old letter to Marty McFly in 1989's Back to the Future Part II, as well as yelling "jackass!" in Happy Gilmore.

In 1999, Flaherty joined the cast of Freaks and Geeks, an NBC hour-long dramedy in which he played Harold Weir, the irascible father of two teens. Despite a dedicated cult following, the show only lasted one season. He made appearances on the CBS sitcom The King of Queens as Father McAndrew, priest at the Heffernan's church. He currently stars on the Bite TV original program called Uncle Joe's Cartoon Playhouse, and serves as a judge on the CBC program Second City's: Next Comedy Legend.

, Flaherty is a member of the faculty at Humber College, where he teaches a comedy writing course. He is also on the program's Advisory Committee. He is also an accomplished pianist.

Flaherty's brothers are comedy writers David and Paul Flaherty (the latter being a writer on SCTV). He has a daughter and a son; Gudrun Flaherty and Gabriel Flaherty.

In season 8 of Family Guy, Joe once again played the Western Union man in "Something, Something, Something, Dark Side".

Celebrities impersonated by Flaherty on SCTV include: Kirk Douglas, Charlton Heston, William F. Buckley, Jack Klugman, Robert Mitchum, Bing Crosby, Don Knotts, Yassir Arafat, Richard Nixon, Alistair Cooke, Slim Whitman, the corpse of Albert Schweitzer, Gregory Peck, Eddie Anderson (as 'Rochester'), Alan Alda, Elvis Presley, Hugh Beaumont, John Huston, Larry Fine, Pope Paul VI, Geraldo Rivera, Art Garfunkel, Broderick Crawford, Jacques Cousteau, Lowell Thomas, Henry Fonda, Marcello Mastroianni, Sylvester Stallone, Shoo Boxx, Paul Bradley, Aaron Copland, Dom DiMaggio, Dick Beddoes, Gavin MacLeod, Prince Philip, Tom Wolfe, Peter O'Toole, Salvador Dalí, Gene Siskel, and musician Paul Revere.

Flaherty appeared in a cameo in the deleted scenes from Anchorman as the salacious News Director who first employs Rita Genkin after her graduation from Syracuse University. He encourages her to wear a swimsuit to do the weather.

Flaherty appeared as an immigration mountie in the "Canadian Road Trip" episode of That '70s Show alongside fellow SCTV member Dave Thomas.

• In the third episode of Freaks and Geeks, "Tricks and Treats", he is dressed up as a vampire, a reference to his character Count Floyd.