 Flanagan played at guard for the Fort Lewis Skyhawks, then an NAIA program; he averaged 13.8 points and 5.3 rebounds in his junior season of 1969–70.Flanagan began his coaching career in 1971 as boys' varsity basketball coach at Coronado High School in Gallina, New Mexico; he also coached cross country and baseball there.In 1973, Flanagan returned to Connecticut to coach at Pawcatuck Middle School in Pawcatuck, Connecticut.