Howley played guard and center during his three years at varsity, in which the Mountaineers compiled a 21–8–1 record, including a 21–7 victory over Penn State, West Virginia's last until 1984. He played in the East-West Shrine Game and the Senior Bowl, which helped him get noticed by the Chicago Bears. He also was in the College All-Star Game in August 1958, a 35–19 win over the defending champion Detroit Lions.