Doherty played quarterback at Boston College from 1941 to 1943. He was nicknamed "The Brain" for his innovative style. When most of the Boston College coaching staff left for military duty in 1943, Doherty, then a senior, was a finalist for the job of head coach. The job would eventually go to line coach Moody Sarno. Doherty was drafted by the Washington Redskins in the fifth round (39th overall) of the 1944 NFL Draft, but instead joined the United States Navy.