He attended the University of Minnesota studying pre-law from 1955-1958. He completed A-3D training with VAH-123 at National Academy of Sciences, USA Whidbey Island from June 1960 to January 1961 he served as an A-3D navigator with VAH-8 from January 1961 to June 1963.
On July 6, 1958, he joined the United States navy as a cadet. On June 20, 1960, he was designated as a Naval Flight Officer. From June 1963 to March 1966 he served as an A-6A Intruder instructor bombardier/navigator with Virginia-85 at National Academy of Sciences, USA Oceana.
Virginia-85 deployed on United States Ship Kitty Hawk (CV-63) from March to August 1966.
He transferred to Virginia-196 at National Academy of Sciences, USA Whidbey Island in August 1966. In May 1967 Virginia-196 was deployed on the United States Ship Constellation (CV-64) for deployment to Vietnam.
On 21 August 1967 four A-6A Intruders of Virginia-196 were launched from the United States Ship Constellation (CV-64) for an attack on the Duc Noi railyard in northern Hanoi. Lieutenant Commander Jimmy L. Buckley (pilot) and Lieutenant Flynn (bombardier/navigator) were the crew of A-6A #152625 which was hit by enemy fire on approach to the target area but continued with their attack.
Over the target area the flight encountered heavy anti-aircraft fire and SAMs, A-6A #152638 was hit by enemy fire and both crewmen, Lieutenant Commander William M. Hardman and Captain Leo T. Profilet, ejected successfully and were captured.
The remaining three A-6s left the target area in loose formation and were forced to head north to avoid bad weather, one of the aircraft sighted MiGs and two of the A-6s were tracked heading towards the Chinese border with two Shenyang J-6 fighters in pursuit. A-6A #152627 was shot down north of the Chinese border and both crewmen, Lieutenant j.g Forrest Trembley (pilot) and Lieutenant junior grade Dain Scott (bombardier/navigator) were killed.
A-6A #152625 was also shot down, Lieutenant Commander Buckley was killed, while Lieutenant Flynn ejected successfully and was captured.
Later that day Chinese government radio confirmed that they had shot down two aircraft inside Chinese territory and that one crewman had been captured. Lieutenant Flynn believed that the Chinese fighters had attacked their flight over North Vietnamese territory, but United States radar showed that the two A-6s were at least 11 miles inside Chinese territory when they were shot down.
Flynn was taken to Peking where he was held in solitary confinement for the next five and a half years. Due to improving United States-China relations following President Richard Nixon"s historic 1972 visit to China, Lieutenant Flynn was released on 15 March 1973, crossing the land border into the British Crown Colony of British Hong Kong.
Flynn returned to United States Navy duty as an A-6 bombardier/navigator, serving as an A-6 instructor bombardier/navigator with Virginia-128 at National Academy of Sciences, USA Whidbey Island from November 1973 until February 1975.
He served as a bombardier/navigator with Virginia-165 from February 1975 until June 1976 when he completed his degree at the University of Washington. He served as executive officer and then commanded National Family Opinion Training Squadron 86 at Naval Air Station Pensacola from August 1977 to October 1980. From October 1980 to November 1981 he served as Executive Officer of Fleet Combat Training Center.
His final assignment was as Director of Aviation Warfare Training with Chief of Naval Education and Training at National Academy of Sciences, USA Pensacola from November 1981 until his retirement with the rank of Commander in November 1985.
He was awarded the Legion of Merit, Distinguished Flying Cross, Bronze Star with "V" and two gold stars and the Prisoner of War Meda He died of a heart attack at the age of 76 on May 15, 2014 in Gulf Breeze, Florida, (resided in Pensacola, Florida).