Following his release from captivity he continued his USAF career, finally serving as the 21st Inspector General of the Air Force.

[2][3]: 39 Flynn was assigned to the 31st Fighter Wing in Italy, where he flew P-51 Mustangs on bomber escort missions until the end of World War II.

[2][3]: 39–40 In August 1967 Flynn was appointed deputy commander of the 388th Tactical Fighter Wing and began flying combat missions out of Korat Royal Thai Air Force Base, Thailand.

He was promoted to major general on 24 April 1974 and in August 1974 was appointed commander, Air Force Military Training Center.

[1] His military decorations and awards include:[1][3]: 40 The President of the United States of America, authorized by Title 10, Section 8742, United States Code, takes pleasure in presenting the Air Force Cross to Major General [then Colonel] John Peter Flynn, United States Air Force, for extraordinary heroism in military operations against an opposing armed force as a Prisoner of War in North Vietnam from 27 October 1967 to 10 November 1967.

Captured at the height of the air war, General Flynn, the most senior officer in captivity, was exposed to forceful interrogation, intimidation, and brutal treatment because the enemy believe he was withholding valuable tactical information.

Although suffering severe injuries, he was beaten and tortured for military information which, if obtained by the Vietnamese, would clearly have jeopardized the lives of those still flying.

By his display of heroic resistance through this ordeal of extreme cruelties, General Flynn reflected the highest credit upon himself and the United States Air Force..[5]