 From 1979 to 1995, Flanagan was the girls' basketball head coach at Eldorado High School in Albuquerque, New Mexico, where he had a record of 401-13 and 11 New Mexico Activities Association Class 4A championships for the years 1980, 1981, 1983, 1984, 1986, 1987, 1989, 1990, 1992, 1993, and 1995.Flanagan was inducted into the Albuquerque Sports Hall of Fame in 1997.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.