Cowan was a member of the Washington Huskies of the University of Washington from 1979 to 1982.[1] He completed six of 19 passes (31.6%) for 109 yards, and one touchdown in 1980.[2] In 1981, he recorded 13 completions on 20 passing attempts (65.0%) for 182 yards, one touchdown, and three interceptions.[2] Cowan completed 64 of 118 passes (54.2%) for 800 yards, eight touchdowns, and four interceptions during his final year at Washington in 1982.[2]
Cowan signed with the BC Lions of the Canadian Football League (CFL) on March 17, 1983.[3] He dressed in three games for the Lions that year as a backup to Roy Dewalt and Joe Paopao, completing five of 21 passes (23.8%) for 53 yards.[4][5] Cowan dressed in all 16 games, starting four, during the 1984 season and totaled 96 completions on 186 passing attempts (51.6%) for 1,434 yards, 13 touchdowns, and ten interceptions.[1][6] He also fumbled six times, losing five of them.[1] His four starts came after Dewalt suffered a broken collarbone.[6][7][8] Cowan dressed in 14 games for the Lions in 1985, backing up Dewalt once again.[9] Cowan completed 43 of 76 passes (56.6%) for 599 yards, six touchdowns, and five interceptions that season.[1] On November 24, 1985, the Lions won the 73rd Grey Cup against the Hamilton Tiger-Cats by a score of 37–24.[10][11][12] He continued his backup role to Dewalt in 1986, dressing in nine games while completing 20 of 47 passes (42.6%) for 271 yards and four interceptions.[13][1]
On August 22, 1986, Cowan was traded to the Toronto Argonauts for the Argonauts' first pick in the 1987 CFL draft.[14] He dressed in nine games for the Argonauts during the 1986 season, recording 20 completions on 48 attempts (41.7%) for 302 yards, two touchdowns, and seven interceptions.[1] He became a free agent after the season.[3]