In 1990, Dunleavy entered his first head coaching job as coach of the Los Angeles Lakers. That season, he led his team to the NBA Finals against the Chicago Bulls and made the playoffs in his second season in LA as well.

He joined the Milwaukee Bucks as head coach prior to the 1992-1993 season and remained with them until the end of the 1995-1996 season, in a dual role as vice-president of basketball operations and head coach. He relinquished his head coaching duties after accepting the job of head coach of the Portland Trail Blazers in 1997.

Dunleavy was named NBA Coach of the Year in 1999 while with the Blazers. He remained in Portland until the end of the 2000-2001 season. He made the playoffs four times in Portland with notable stars Rasheed Wallace, Damon Stoudamire, and Arvydas Sabonis.

He joined the Clippers in 2003 and was a candidate for the 2006 Coach of the Year. He led the Clippers to the second round of the playoffs. It was their first playoff berth since 1997, and the franchise's first series win since a 1977 first-round victory while the team was still playing in Buffalo.

He worked for TNT in 2008 calling NBA playoff games.

His son, Mike Dunleavy Jr., won a NCAA championship with the Duke Blue Devils and has played for various NBA teams.