Allen played college baseball for the Boilermakers, where he twice named Team MVP. A winner of 6 varsity letters, Allen was also a quarterback on the football team, selected as Team MVP in 1960. He platooned at quarterback in 1959, leading the Boilermakers to a 5-2-2 record and six weeks in the Top 15. Earning the starting job in 1960, Allen led the Boilermakers to a record of 4-4-1 (2-4 Big Ten) and wins over #12 Notre Dame, Ohio State and #1 Minnesota, the AP and UPI National Champion. The Minnesota and Notre Dame wins were both road wins, while the win over Ohio State earned Allen Sports Illustrated's Offensive back of the Week. Purdue spent 5 weeks in the Top 15 and finished the season at #19. Allen was selected for the Blue–Gray Game; throwing 3 touchdowns and led the Blue squad to a 35-7 victory over the Gray squad, quarterbacked by Fran Tarkenton. Allen was the leading passer for Purdue during the 1959 and 1960 seasons and was also the team leader in total offense. He was selected as an All-American shortstop in , he signed with the Twins and played 80 games for Class A Charlotte before being promoted to Major League Baseball.