[2] Dougherty began his collegiate career at the College of the Sequoias, where he also played basketball and baseball.
At 5-9, he intended to pursue a baseball career instead of football before he suffered a back injury.
[4] In his first season at Boston University, he was named the Yankee Conference Offensive Player of the Year after completing 212-of-386 passes for 2,875 yards and 18 touchdowns while also rushing for 11 touchdowns as the Terriers went undefeated in the regular season.
As a senior Dougherty repeated as the conference Offensive Player of the Year after he completed 262-of 440 passes for 3,596 yards and 24 touchdowns as BU went 9-3 and earned an at-large bid to the 1994 NCAA Division I-AA Playoff.
[5] Dougherty was signed by the Toronto Argonauts of the Canadian Football League (CFL) on March 17, 1995.