As women's basketball coach at the University of New Mexico, Flanagan coached 508 collegiate games, which as of March 7, 2014, is a feat no coach has done in New Mexico basketball history. As of March 2014, he holds the title of most wins by any coach, men's or women's, at the school with 340 victories. He passed former UNM Men's Basketball coach Dave Bliss's 246 wins on December 9, 2006. From 1998 to 2010, Flanagan's teams made the NCAA Tournament or Women's National Invitation Tournament (WNIT) every year. Flanagan's New Mexico teams made seven NCAA Tournaments and six WNITs.