[3][5] Flanagan graduated from the Massachusetts Maritime Academy in 1964 with a Bachelor of Science degree in marine transportation and an ensign's commission in the Naval Reserve, joining the Merchant Marine and working for American Export-Isbrandtsen Lines out of New York, where he achieved the grade of second mate.

After three years of service with American Export Lines, Flanagan reported for active duty with the United States Navy on May 15, 1967 as a lieutenant (junior grade).

Flannagan commanded the guided missile destroyer—the lead ship of her class—on her first deployment to the Mediterranean Sea and the Indian Ocean.

At the end of his tenure in this position, he was responsible for more than 200,000 Navy and Marine Corps personnel, 220 vessels, 1,500 aircraft, and 27 shore installations.

Flanagan stepped down from commanding the Atlantic Fleet on December 20, 1996, and retired shortly thereafter after approximately thirty years of naval service.