From 1979 to 1989, Berry was the head men's basketball coach at San Jose State. For the San Jose State Spartans, Berry had a 142-144 record, then the Spartans' second-highest win total under one coach. Under Berry, San Jose State had a 17-12 record in the 1979–80 season, won the 1980 PCAA tournament, and made the 1980 NCAA tournament. In a 21-9 season in 1980–81, San Jose State qualified for the 1981 National Invitation Tournament. San Jose State also had three straight seasons over .500 from 1984 to 1987. However, the 1988–89 Spartans finished 5-23. In January 1989, when the team was 5-11, 10 of the 14 players on the Spartans men's basketball team accused Berry of "mental cruelty" and refused to play or practice under Berry as coach. However, the players declined to provide specific examples. Berry then organized a new team of walk-on athletes, including star football player Johnny Johnson. San Jose State dismissed Berry after the season.
Berry was an assistant under Tim Floyd until Floyd resigned on Christmas Eve (December 24) of 2001, when the Bulls named Berry as interim head coach. Berry coached two games, both losses, and Bill Cartwright became permanent head coach effective December 28. On September 7, 2006, the Washington Wizards announced that Bill Berry would join the team as an assistant coach to head coach Eddie Jordan.
Bill Berry has been married to Clarice "Reese" Berry since 1963 and had two children. The Berry family lived in Morgan Hill, California during Bill Berry's tenure at San Jose State. Their son Ricky Berry (1964–1989) played at San Jose State under Bill Berry, and Ricky Berry went on to play for the NBA team Sacramento Kings before committing suicide in 1989.