Poindexter was commisioned following graduation from the Georgia Institute of Technology in 1986. After a short tour of duty at the Hypervelocity Wind Tunnel Facility, Naval Surface Weapons Center, White Oak, Maryland, Poindexter reported for flight training in Pensacola, Florida. He was designated a Naval Aviator in 1988 and reported to Fighter Squadron 124, Naval Air Station Miramar, California, for transition to the F-14 Tomcat. Following his initial training, Poindexter was assigned to Fighter Squadron 211, also at Miramar, and made two deployments to the Arabian Gulf during Operations Desert Storm and Southern Watch. While attached to VF-211, Poindexter was designated as a Wing Qualified Landing Signal Officer. During his second deployment in 1993, he was selected to attend the Naval Postgraduate School/U.S. Naval Test Pilot School Cooperative Program. Following graduation in December 1995, Poindexter was assigned as a Test Pilot and Project Officer at the Naval Strike Aircraft Test Squadron (NSATS), Naval Air Station (NAS) Patuxent River, Maryland. While at NSATS, Poindexter was assigned as the lead test pilot for the F-14 Digital Flight Control System where he logged the first carrier landing and catapult launch of an F-14 with the upgraded flight controls. He also flew numerous high angle of attack/departure tests, weapons separation tests and carrier suitability trials. Following his tour at Patuxent River, Poindexter reported to Fighter Squadron 32, NAS Oceana, Virginia where he was serving as a department head when he was selected for Astronaut training.
Poindexter has more than 2,000 hours in over 30 aircraft types and has logged over 450 carrier landings.