John R. Allen, Jr. was born in Louisville, Kentucky, in 1935. Allen was commissioned in December 1959 and assigned to Little Rock Air Force Base, Arkansas, as a B-47 co-pilot. He was transferred to the 393rd Bombardment Squadron as a B-47 commander (1964).

He was then assigned to the 20th Bombardment Squadron serving as chief of the Standardization Division (1966). Between 1969 and 1971, he flew 150 B-52 combat missions during three temporary duty tours in Southeast Asia and served as chief of the Tactical Evaluation Division, 8th Air Force, Andersen Air Force Base, Guam. Allen then served as the Arc Light liaison officer at Headquarters U.S. Air Force, Washington, D.C. (1972).

Allen was an air operations staff officer at Headquarters Strategic Air Command (SAC), Offutt Air Force Base, Nebraska (1974). His varied duties included the certification of Navy sea mines for use on B-52D's and feasibility tests of B-52 high-altitude laser-guided bomb delivery.

He then became chief of the Aircraft and Weapons Test Branch and, later, executive officer to the deputy chief of staff for operations, also at SAC headquarters.

Allen assumed command of the 46th Bombardment Squadron, Grand Forks Air Force Base (1977). He was assigned to the Air Staff at Air Force headquarters in August 1978 as one of two action officers who presented Air Force positions regarding the Strategic Arms Limitation Talks to the Joint Staff.

He transferred to the 92nd Bombardment Wing, Fairchild Air Force Base, Washington, as vice commander in January 1982 and in August 1982 assumed command of the wing.

In September 1984, Allen was assigned as the senior military adviser to the director, U.S. Arms Control and Disarmament Agency, Washington, D.C., where he provided high-level liaison with the Office of the Secretary of Defense and the Joint Chiefs of Staff in policy formulation, arms control negotiations and agency operations.

In June 1986, he was assigned as commander of SAC's 45th Air Division, consisting of FB-111s at Pease Air Force Base, and Plattsburgh Air Force Base, New York; and B-52G's at Loring Air Force Base, Maine. In September 1987, Allen became vice commander, Sacramento Air Logistics Center, Air Force Logistics Command. In August 1989, he became the vice commander of Oklahoma City Air Logistics Center, Air Force Logistics Command, Tinker Air Force Base.

The general is a command pilot with more than 6,000 flying hours in B-47’s, FB-111s, B-52’s, KC-135s and T-39s.

Allen's awards include the Defense Superior Service Medal, Legion of Merit, Distinguished Flying Cross, Defense Meritorious Service Medal, Meritorious Service Medal with oak leaf cluster, Air Medal with six oak leaf clusters, Air Force Commendation Medal with oak leaf cluster and Combat Readiness Medal.

He retired after 31 years of service on October 1, 1990.