Fahey was born in Olean, New York, the sixth of 13 siblings in an Irish American family. His mother, Jane, was a homemaker, and his father, Frank Fahey, worked at a clothing store. Fahey was raised in Buffalo, New York, from the age of ten and attended Father Baker's High School there. Fahey left home at the age of 17, subsequently hitchhiking to Alaska. He later backpacked through Europe, and worked on an Israeli kibbutz.
Fahey started performing when he won a full scholarship to dance at the Joffrey Ballet School at the age of 25. He performed in theaters across the United States and on Broadway. He landed his first major role in television playing Gary Corelli on the soap opera One Life to Live.
In 1985 he received his first major role in film, playing "Tyree" in Silverado. In 1986 he starred in Psycho III as Duane Duke, a money desperate guitarist. That same year, Fahey guest starred on the Season 3 premiere of Miami Vice as gun dealer "Eddie Kaye", famously destroying Detective Sonny Crockett's Ferrari Daytona.
He played "Thorold Stone" in the film Revelation. Fahey later starred alongside Pierce Brosnan in The Lawnmower Man.
In 1990 he starred alongside Marisa Tomei in Parker Kane and Clint Eastwood in the Eastwood directed White Hunter, Black Heart. In 1995 he starred as "Winston McBride" on ABC's The Marshal. In 2007, he appeared in the Robert Rodriguez film Planet Terror and starred in Messages with Bruce Payne.
Fahey appeared as daredevil "Dutch the Clutch" in an episode of Psych in the beginning of the third season of the show.
Fahey played recurring character, Frank Lapidus, the airplane and helicopter pilot of the research team sent to the island in the fourth, fifth, and as a regular character for the sixth season of Lost.
In 2010 he had a major role in the Robert Rodriguez action film Machete.
In 2013 a new production of the classic play Twelve Angry Men took place at the Garrick Theatre in London, running until March 2014. Fahey played the part of the last juror in the story to change his vote to not guilty. Other notable actors appearing in this production were Martin Shaw who played the part of juror number 8 (a role made famous in the 1957 film by Henry Fonda), Robert Vaughn and Nick Moran.