Following retirement as a player, O'Connell served as head coach of the San Diego Gulls of the International Hockey League (IHL) in 1990–91. Despite a losing record, Harry Sinden hired his protégé to coach the Bruins' top minor league affiliate, the Providence Bruins. O'Connell was then named the Bruins' assistant general manager in 1994, also becoming vice president of hockey operations in 1998 and alternate governor in 2000. The Bruins named O'Connell vice president and general manager on November 1, 2000, and he later signed a five-year contract extension on June 21, 2002. He was however fired from the job on March 25, 2006 following a controversial number of player trades that did not work out well for the Bruins. Notably, O'Connell decided to trade high-scoring center Joe Thornton.