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. At Pawcatabuck, Flanagan had a 15–0 season. Flanagan returned to the Southwest in 1975 as boys' varsity basketball coach at Window Rock High School in Fort Defiance, Arizona. Window Rock went 75–25 and made the state tournament every year under Flanagan, including as state runner-up in 1978.