Johnson received his commission from the United States Air Force Academy in May 1984 and was designated an Air Force pilot in May 1986 at Reese Air Force Base, Texas. He was retained as a T-38A instructor pilot at Reese until 1989, when he was selected for an F-15E Eagle assignment. In March 1990, he reported to the 461st F-15E Replacement Training Unit at Luke Air Force Base, Phoenix, Arizona for initial F-15E training. After completion, he was assigned to the 335th Fighter Squadron, 4th Fighter Wing at Seymour Johnson Air Force Base, North Carolina. Immediately after he was designated "mission ready" in December 1990, Johnson deployed to Al Kharj, Saudi Arabia, flying 34 combat missions in support of OPERATION DESERT STORM. In December 1992, he was again deployed to Saudi Arabia for three months, flying an additional 27 combat missions in support of OPERATION SOUTHERN WATCH. In 1993, he was selected for Air Force Test Pilot School at Edwards Air Force Base, California, where he graduated in December 1994. After graduation, he was assigned to the 445th Flight Test Squadron at Edwards, where he was a project test pilot, F-15C/E and T-38 instructor/evaluator, program manager, and assistant operations officer. In August 1997, he was assigned to Maxwell Air Force Base, Alabama, to attend Air Command and Staff College in residence. Just prior to graduation in June 1998, Johnson learned of his selection for astronaut training.
He has logged over 2,700 flight hours in more than 30 different aircraft.