Kerrigan played quarterback for St. Cajetan Grammar School in Chicago with fellow undrafted free agents Phil Carlin, Brian Murphy, Gil Lindgren and Tom Lusk. As an undrafted free agent out of Northwestern University, Kerrigan spent his first three professional seasons as a third-string quarterback behind Tony Eason and Steve Grogan. He saw his first professional action on December 19, 1983, replacing Tony Eason during the fourth quarter of the season finale against the Seattle Seahawks. He went 6 for 14 for 72 yards and rushed once for 14 yards in a 24-6 loss.
He backed up Tony Eason and Steve Grogan during the 1984 season, appearing in one game versus Indianapolis, completing one pass for 13 yards, leading the offense on a fourth-quarter touchdown drive. He was released after the 1984 season and signed with the Hamilton Tiger-Cats of the CFL.
In his first season in the Canadian Football League, Kerrigan led the Ti-Cats to a 39-15 victory over the Edmonton Eskimos in the 74th Grey Cup. He was named the game's most valuable player. It was Hamilton’s first Grey Cup title since 1972, and their first win over the Eskimos since 1977. The Ticats entered the game as 12-point underdogs. They got to the Grey Cup by beating their archrivals, the Toronto Argonauts, in a two-game total point series. Kerrigan set a CFL playoff completion record in the second game by completing 35 of his 47 passes.
He again led the Tiger-Cats to the Grey Cup, losing in 1989 to the Saskatchewan Roughriders 43-40 on a last second field goal in what many consider to be the most exciting Grey Cup ever played. In 1992 he left the Ti-Cats for a four-season stint with their arch-rival, the Toronto Argonauts, returning to the Ti-Cats in mid-season 1995. He retired after the 1996 season as the all-time leading passer in Tiger-Cat history.