He is best known for his work on the Canadian sketch comedy SCTV from 1976 to 1984 (on which he also served as a writer), his role as Harold Weir on Freaks and Geeks (1999), and as the heckler in Happy Gilmore (1996).

[1] Flaherty moved to Chicago, where he started his comedy career in 1969 with the Second City Theater as Joe O'Flaherty and would work with future stars such as John Belushi and Harold Ramis.

[13] In 1989, he played a guest role in Married... with Children in the season-four episode "Tooth or Consequences", as a dentist who must repair Al Bundy's teeth.

[11][17] In 1999, Flaherty joined the cast of Freaks and Geeks, an NBC hour-long dramedy set in the 1980–1981 academic year, in which he played Harold Weir, the "imperfect perfect" father of two teens.

[19] Flaherty made appearances on the CBS sitcom The King of Queens as Father McAndrew, the priest at the Heffernans' church.

[20] Beginning in 2004, Flaherty was artist-in-residence at Humber College's School of Creative and Performing Arts in Toronto, where he taught a comedy writing course.

He previously helped found the school's comedy writing and performance program serving as its artistic director.

[26][27][28] Flaherty impersonated a number of celebrities, including Kirk Douglas, Richard Nixon, Gregory Peck, Alan Alda, Bing Crosby, Gavin McLeod and Elvis Presley.