Born in Cambridge, Massachusetts and raised in the Mayberry Village community of New Hartford, Connecticut,[1][3] Flanagan graduated from Cornwall Academy after attending East Hartford High School for three years and earned a basketball scholarship to Hartwick College, but he dropped out after one year.
[4] Flanagan worked in Hartford before moving to Durango, Colorado to enroll at Fort Lewis College in 1967.
[5] 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.
[4][7] Flanagan returned to the Southwest in 1975 as boys' varsity basketball coach at Window Rock High School in Fort Defiance, Arizona.
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.