Thomas Van Kirk said his father died Monday at home in Stone Mountain, Ga.
Van Kirk, like other members of the Enola Gay crew, said he never had any doubts about his actions. In an interview with the New York Times on the 50th anniversary of the Hiroshima raid, he said he felt "a sense of relief" when he saw the city covered with a pall of black smoke on Aug. 6, 1945.
In an interview for the 2000 book Duty by Bob Greene, Van Kirk said there was "a sense that the war was over or would be soon."
Three days after the Hiroshima raid, a plutonium bomb was dropped on Nagasaki. Japan surrendered Aug. 15, ending World War II.
Van Kirk, nicknamed Dutch, was a native of Pennsylvania. He dropped out of college to join the Army Air Force in 1941.
Paul W. Tibbets Jr., who later commanded the Enola Gay, named after his mother, selected Van Kirk and Thomas W. Ferrebee for the crew of his B-17. The crew led raids on Europe and flew Gen. Dwight Eisenhower to Gibraltar.
Van Kirk was back in the United States training air crew when he and Ferrebee were again picked by Tibbets, this time for a mission he could not describe in detail.
"He told me, 'We're going to do something that I can't tell you about right now, but if it works, it will end or significantly shorten the war. 'And I thought, 'Oh, yeah, buddy, I've heard that before,'" Van Kirk told Time magazine in 2005.
Van Kirk, a captain at the time of the Hiroshima raid, left the Army Air Force in 1946 with the rank of major. He was awarded the Silver Star and Distinguished Flying Cross.
He went to work for DuPont after earning bachelor's and master's degrees in chemical engineering at Bucknell University.