On April 4, 2011, Flanagan announced his resignation, following a 13–18 season and with a year remaining on his contract. He finished his coaching career with the Lobos with a record of 340 wins to 168 losses. Prior to his resignation, five freshmen players left the team. Flanagan responded: "It wasn't fair to the program for me to stay and try to recruit multiple players with one year left on my contract." With that resignation, Flanagan retired from coaching. Assistant coach Yvonne Sanchez, who had been an assistant coach under Flanagan since 2000, succeeded Flanagan as head coach on April 22, 2011.