Engle received his commission in the Air Force through the Reserve Officers Training Program at the University of Kansas, and entered flying school in 1957. He served with the 474th Fighter Day Squadron and the 309th Tactical Fighter Squadron at George Air Force Base, California. He is a graduate of the USAF Test Pilot School and the Air Force Aerospace Research Pilot School. Engle was a test pilot in the X-15 research program at Edwards Air Force Base, California, from June 1963 until his assignment to the Lyndon B. Johnson Space Center. Three of his 16 flights in the X-15 exceeded an altitude of 50 miles (80 km) (the altitude that qualifies a pilot for astronaut rating). Prior to that time, he was a test pilot in the Fighter Test Group at Edwards.
He has flown over 155 different types of aircraft (25 different fighters) during his career: logging more than 12,400 hours flight time; 9,000 in jet aircraft. Engle was one of the 19 astronauts selected by NASA in April 1966. He was back-up lunar module pilot for the Apollo 14 mission and was due to land on the moon as lunar module pilot for Apollo 17, but was replaced by geologist Harrison Schmitt after Apollo 18 was cancelled with pressure from the scientific community to have a scientist explore the Moon, and not just test pilots who had been given geology training.
He was commander of one of the two crews that flew the Space Shuttle Approach and Landing Test Flights from June through October 1977. The Space Shuttle Enterprise was carried to 25,000 feet on top of the Boeing 747 carrier aircraft, and then released for its two minute glide flight to landing. In this series of flight tests, he evaluated the Orbiter handling qualities and landing characteristics, and obtained the stability and control, and performance data in the subsonic flight envelope for the Space Shuttle. Engle and Richard Truly flew the second flight of the Space Shuttle that was boosted into orbit. He was the back-up commander for STS-1, the first orbital test flight of Space Shuttle Columbia. He was spacecraft commander on STS-2 and STS-51-I, and has logged over 225 hours in space.
He served as Deputy Associate Administrator for Manned Space Flight at NASA headquarters from March 1982 to December 1982. He retained his flight astronaut status and returned to the Johnson Space Center in January 1983. He also participated in the Challenger disaster investigation in 1986, and would do other consulting work on the Shuttle well into the 1990s.
Joe Engle retired from the USAF on November 30, 1986. On December 1, 1986 he was appointed to the Kansas Air National Guard and subsequently promoted to the rank of Brigadier General. In 1992, he was inducted into the Aerospace Walk of Honor. On July 21, 2001, Engle was enshrined at Dayton, Ohio, in the National Aviation Hall of Fame class of 2001, along with USAF ace Robin Olds, Marine Corps ace Marion Carl, and Albert Ueltschi.
He is currently an aerospace and sporting goods consultant, and continues an active flying career in high performance aircraft.