Born on November 14, 1933, and raised in Biloxi, Mississippi, Haise attended Biloxi High School, from which he graduated in 1950, and Perkinston Junior College, with original aims of a career in journalism, receiving an Associate of Arts degree in 1952. He was a Boy Scout, earning the rank of Star Scout. Eligible for the draft and despite being apprehensive of flying, he joined the naval aviation cadet training program. Haise underwent Naval Aviator training from 1952 to 1954 and served as a U.S. Marine Corps fighter pilot at MCAS Cherry Point, North Carolina, from March 1954 to September 1956.
After his military service, Haise returned to school and graduated with a Bachelor of Science degree with honors in Aeronautical Engineering from the University of Oklahoma in 1959, concurrently serving in the Oklahoma Air National Guard, as a fighter interceptor pilot with the 185th Fighter Interceptor Squadron. He then worked for the newly created NASA, first as a research pilot at the Lewis Research Center near Cleveland. His air guard unit was called up during the Berlin Crisis of 1961 and he served ten months as a fighter pilot in the United States Air Force. He was a tactical fighter pilot and chief of the 164th Standardization-Evaluation Flight of the 164th Tactical Fighter Squadron at Mansfield Lahm Air National Guard Base, Ohio.
Haise completed post-graduate courses at the Aerospace Research Pilot School at Edwards Air Force Base, California in 1964, and the Harvard Business School's Advanced Management Program in 1972. He received an honorary Doctorate of Science from Western Michigan University in 1970.
In 1966, Haise was one of 19 new astronauts selected for NASA Astronaut Group 5. He had already been working with NASA for several years as a civilian research pilot. He was the first astronaut among his class to be assigned to a mission, serving as backup Lunar Module Pilot for both Apollo 8 and Apollo 11.
Haise flew as the Lunar Module Pilot on the aborted Apollo 13 lunar mission in 1970. Due to the free return trajectory on this mission, Haise, Jim Lovell and Jack Swigert, the other two astronauts on Apollo 13, likely hold the record for the farthest distance from the Earth ever traveled by human beings. During this flight Haise developed a urinary tract infection and later kidney infections. These caused him to be in pain for most of the trip.