In April 1990, Johnson was accepted as an aerospace engineer and research pilot at the NASA JSC Aircraft Operations Division, Ellington Field, Texas. He qualified as a T-38 Talon instructor pilot, functional check flight and examiner pilot, as well as Gulfstream I aircraft commander, WB-57F Canberra high altitude research pilot and KC-135 co-pilot. Additionally, he conducted flight test programs in the T-38 aircraft including JET-A airstart testing, T-38N avionics upgrade testing and the first flight of the T-38 inlet redesign aircraft. In 1994 he assumed duties as the Chief, Maintenance & Engineering Branch responsible for all maintenance and engineering modifications on NASA JSC's 44 aircraft.