After graduation, Kelly was commissioned as an ensign in the United States Navy. He completed his initial flight school at NAS Pensacola, where he flew the T-34 Mentor propeller driven trainer plane, after which he was selected to fly jets. In 1988, he moved to Beeville, Texas, for jet training Naval Air Station Chase Field, where he trained on the T-2 Buckeye and the A-4 Skyhawk. He graduated as a naval aviator in 1989, and was assigned to fly the F-14 Tomcat. He reported to VF-101 at Naval Air Station Oceana, Virginia, for initial F-14 training. Upon completion of this training in September 1990, he was assigned to VF-143, and deployed to the North Atlantic and Persian Gulf aboard the aircraft carrier .