Sonny Carter was born in Macon, Georgia, but considered Warner Robins, Georgia, to be his hometown. He graduated from Lanier High School in Macon in 1965, and during his high school years was involved actively in Macon-based Troop 19 of the Boy Scouts of America, where he also served a term as Senior Patrol Leader, the highest leadership position for a young man in that BSA troop. He received a bachelor of arts degree in chemistry from Emory University in Atlanta in 1969 and a doctor of medicine degree from there in 1973. During his time at Emory, Carter was a brother in the Alpha Tau Omega Fraternity. After completing medical school in 1973, Carter completed internship in internal medicine at Grady Memorial Hospital in Atlanta.

Carter played collegiate soccer and ran track while an undergraduate at Emory University. During his senior season he was captain and most valuable player of the soccer team. In addition to his intercollegiate athletic career, Carter was an intramural wrestling champion. Carter played professional soccer while he attended medical school. In 1970 he signed with the Atlanta Chiefs of the North American Soccer League, for whom he played three seasons.

In 1974 he entered the U.S. Navy and completed flight surgeon school in Pensacola, Florida. After serving tours as a flight surgeon with the 1st and 3rd Marine Aircraft Wings, he returned to flight training at Beeville, Texas, and was designated a Naval Aviator on April 28, 1978. He was assigned as the senior medical officer of the USS Forrestal, and in March 1979 completed F-4 training at VMFAT-101 in Marine Corps Air Station Yuma, Arizona. He was subsequently reassigned as a fighter pilot, flying F-4 Phantoms with Marine Fighter Attack Squadron 333 (VMFA-333) at MCAS Beaufort, South Carolina. In 1981 he completed a nine-month Mediterranean cruise aboard USS Forrestal with VMFA-115. In September 1982 he attended U.S. Navy Fighter Weapons School (TOPGUN) and then served as the 2nd Marine Aircraft Wing standardization officer and F-4 combat readiness evaluator at MCAS Cherry Point, North Carolina. He then attended the U.S. Naval Test Pilot School, graduating in June 1984. He has logged 3,000 flying hours and 160 carrier landings.

Selected by NASA in May 1984, Dr. Carter became an astronaut in June 1985, qualified for assignment as a mission specialist on future Space Shuttle flight crews. He was assigned as Extra-vehicular activity (EVA) Representative for the Mission Development Branch of the Astronaut Office when selected to the crew of STS-33. The STS-33 crew launched from Kennedy Space Center, Florida, at night on November 22, 1989, aboard the Space Shuttle Discovery. The mission carried Department of Defense payloads and other secondary payloads. After 79 orbits of the earth, this five-day mission concluded on November 27, 1989 with a hard surface landing on Runway 04 at Edwards Air Force Base, California. Carter logged 120 hours in space.  At the time of his death, Carter was assigned as a mission specialist on the crew of STS-42, the first International Microgravity Laboratory (IML-1).  Carter died in the April 5, 1991 crash of Atlantic Southeast Airlines Flight 2311 in Brunswick, Georgia. He was aboard the commercial airplane traveling for NASA.