After the 1960 Olympics Cleary retired as a player and became an ice hockey official for several years before returning to Harvard in 1968 to coach the freshman squad. Bill was quickly promoted to assistant coach of the varsity team and then became the head coach in 1971 when Cooney Weiland retired. Cleary's teams got off to a fast start with a top two finishing in each of his first four years. Though he couldn't manage to win a tournament in the time (conference or national) Cleary had established himself enough to carry through a down period in the late 1970s.