In 1946, Woolpert was hired as basketball coach for St. Ignatius College Preparatory in San Francisco, where he posted a 63–29 (.685) record in his four years as coach. Upon Pete Newell's departure for Michigan State University, the University of San Francisco hired Woolpert to succeed Newell. He assumed both the posts of men's basketball coach and athletic director.
During his tenure at USF, Woolpert posted a 153–78 (.662) record, including a 60-game win streak that at the time was the longest in college basketball, surpassed later by John Wooden's 88 straight wins at UCLA. Woolpert's teams, anchored by Bill Russell, K. C. Jones, Gene Brown, and Mike Farmer, were known for their defense and held opponents below 60 points on 47 different occasions. USF won the NCAA tournament in 1955 and 1956, and finished third in 1957. At the time the youngest college basketball coach to win a national championship, Woolpert also won Coach of the Year honors in 1955 and 1956.
National champion
Postseason invitational champion
Conference regular season champion
Conference regular season and conference tournament champion
Division regular season champion
Division regular season and conference tournament champion
Conference tournament champion