Joseph Milligan was born in 1941 in Grandin, New Jersey. He was commissioned through the Air Force ROTC program at Rutgers University on June 5, 1963, and went on active duty beginning April 17, 1964. Lt Milligan then attended Undergraduate Pilot Training and was awarded his pilot wings at Vance AFB, Oklahoma, on May 13, 1965, followed by F-4 Phantom II Combat Crew Training and Pilot Systems Operator training. He next served with the 40th Tactical Fighter Squadron at Eglin AFB, Florida, from September 1965 to February 1966, followed by service at the Fighter Weapons School at Nellis AFB, Nevada, where he participated in a top-secret F-4C Wild Weasel program from February to November 1966. Lt Milligan deployed to Southeast Asia with the 433rd Tactical Fighter Squadron at Ubon Royal Thai AFB, Thailand, in November 1966, and was forced to eject over North Vietnam while flying his 113th combat mission on May 20, 1967. He was immediately captured and after spending 2,101 days in captivity he was released during Operation Homecoming on February 18, 1973. He was briefly hospitalized at Westover AFB, Massachusetts, and then received an Air Force Institute of Technology assignment to Rutgers University to obtain his Masters Degree in Animal Science in 1975, and his PhD in Nutrition and Physiology in 1979. Also in 1979, Col Milligan completed his Doctor of Veterinary Medicine degree from Cornell University, and then served with the Air Force Occupational and Environmental Health Laboratory at Brooks AFB, Texas, from June 1979 to August 1983. His next assignment was as Chief of the Chemical Defense Division with Headquarters Aerospace Medical Division, also at Brooks AFB, from September 1983 to June 1985. His final assignment was with Air Force Systems Command at Andrews AFB, Maryland, where he served as Director of Life Sciences, Deputy Chief of Staff for Medical and Life Sciences, Director of Human Systems, Director of Combat Support, and then as Deputy Chief of Staff for Technology and Requirements Planning, where he served from July 1985 until his retirement from the Air Force on September 30, 1988.

His Silver Star Citation reads:

For the Period 20 May 1967 to 28 May 1967. This officer distinguished himself by gallantry and intrepidity in action in connection with military operations against an opposing armed force during the above period while a Prisoner of War in North Vietnam. Ignoring international agreements on treatment of prisoners of war, the enemy resorted to mental and physical cruelties to obtain information, confessions, and propaganda materials. This individual resisted their demands by calling upon his deepest inner strengths in a manner which reflected his devotion to duty and great credit upon himself and the United States Air Force.