Cowan's long-time association with lacrosse began at Friends' School in Baltimore, where he was a standout midfielder. In 1963, he helped the team win the Maryland Scholastic Association Championship. He remained in Baltimore for his collegiate career at Johns Hopkins, and played on three consecutive championship teams from 1967-1969.
Cowan earned first team All-America honors each of those three years, and in both 1968 and 1969 received the prestigious Turnbull Award as the nation's outstanding attackman. In 1969, he was also the first recipient of the Enners Award given to the nation's outstanding player. He was selected to play in the annual North/South game in 1969. He continued at Hopkins for 14 years as an assistant coach, and played for Mt. Washington Lacrosse Club in 1970-71. Cowan also served on the board of directors of the Lacrosse Foundation.