After the war, Donnelly became a Navy civil service employee. He was assigned to aircraft and ordnance testing at the Naval Air Ordnance Test Station at Chincoteague Island, Virginia and the Naval Air Station Patuxent River, Mayland, where he first met Alan Shepard, Pete Conrad, John Young, Jim Lovell and other future astronauts. In 1951, he was awarded an electronic engineer-equivalent degree by the U.S. Civil Service Commission.
