In his first five years coaching at Creighton, the team made the WNIT three times, and the NCAA Tournament in 2012. In 2004, Creighton won the 2004 WNIT Championship. In his first season, he won 24games, the most ever by a Creighton rookie head coach. Flanery previously served as an assistant at Creighton for 11 years. He also served as an assistant basketball coach at Loras College.