From 1958 through 1965, Hofman managed in minor league baseball with the San Francisco Giants and Kansas City Athletics organizations. In 1966, former teammate Alvin Dark (the shortstop for most of Hofman's tenure with the Giants) was named manager of the Athletics, and he added Hofman to his coaching staff. Hofman would go on to coach in the American League for 12 seasons (1966–72; 1974–78) with the Athletics in both Kansas City and Oakland, the Washington Senators and Cleveland Indians. He was a coach, under Dark, on Oakland's 1974 world championship team. After his coaching career, Hofman briefly was Oakland's traveling secretary and, during the 1980s, he served as director of scouting and player development of the New York Yankees. He compiled a record of 574 victories and 599 defeats (.489) as a minor league manager.