In 1960, Petrone was seconded to NASA. There, Petrone presided over the development of Saturn V launch operations, dubbing the period of preparation leading up to each launch "five-month marathons". He oversaw construction of all the launch elements of the Apollo program at Kennedy Space Center, including Launch Complex 39, the Vehicle Assembly Building, and the Crawler-Transporter, all of which were later modified for Space Shuttle operations. After his retirement from the U.S. Army in 1966 he continued to work for NASA as a civilian, being promoted to director of launch operations at KSC in July 1966. In September 1969, shortly after the Apollo 11 mission, he was appointed director of the entire Apollo program at NASA Headquarters. In 1972, Petrone was assigned additional responsibilities as program director of the NASA portion of the U.S. and the Soviet Union joint Apollo-Soyuz Test Project.