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Joseph Shanahan enlisted in the U.S. Air Force on October 22, 1956, and served as an Admin Clerk until entering Officer Training School in September 1960. Staff Sergeant Shanahan was commissioned a second lieutenant at Lackland AFB, Texas, on December 20, 1960, and then attended Undergraduate Navigator Training at Harlingen AFB, Texas, from December 1960 to October 1961. His next assignment was as a C-124 Globemaster II Navigator with the 15th Air Transport Squadron at Dover AFB, Delaware, from November 1961 to March 1963, followed by service as a C-123 Provider Navigator with the 319th Troop Carrier Squadron (redesignated 319th Air Commando Squadron on November 8, 1964) at Eglin Air Force Auxiliary Field No. 9, Florida, from March 1963 to July 1965. Captain Shanahan served as a Navigator Flight Examiner with the 1st Air Commando Wing at Eglin Air Force Auxiliary Field 9 from July to November 1965, and then with the 4410th Combat Crew Training Wing and the 4408th Combat Crew Training Squadron at Eglin Air Force Auxiliary Field 9 from December 1965 to October 1967. He next attended Navigator Reconnaissance Upgrade Training from October to November 1967, followed by RF-4C Phantom II Tactical Reconnaissance training from December 1967 to April 1968. Captain Shanahan served as an RF-4C Navigator Systems Operator with the 14th Tactical Reconnaissance Squadron at Udorn Royal Thai AFB, Thailand, from June 1968 until he was forced to eject from his stricken aircraft over North Vietnam and was taken as a Prisoner of War on August 15, 1968.

Major Shanahan was released during Operation Homecoming on March 14, 1973. He was briefly hospitalized to recover from his injuries at Wright Patterson AFB, Ohio, and then received an Air Force Institute of Technology assignment to complete his degree program at the University of Arizona in Tucson, Arizona. Colonel Shanahan served as Assistant Chief of the Training Evaluation Division with the 3400th Technical Training Wing, Director of Personnel of the 3415th Air Base Group, and then Deputy Base Commander with the 3415th Air Base Group, at Lowry AFB, Colorado, from June 1977 to May 1981, followed by service as Base Commander of the 3300th Technical Training Wing at Keesler AFB, Mississippi, from May 1981 to January 1983. He served as Vice Center Commander of Chanute Technical Training Center at Chanute AFB, Illinois, and then Assistant Chief of Staff/Technical Training with Headquarters Air Training Command at Randolph AFB, Texas, from January 1983 to January 1987. Colonel Shanahan's final assignment was with Headquarters U.S. Air Force in the Pentagon from January 1987 until his retirement from the Air Force on January 1, 1990.
- Silver Star
- Defense Superior Service Medal
- Legion of Merit (3)
- Distinguished Flying Cross
- Bronze Star
- Prisoner of War Medal