Flynn was commissioned in the U.S. Army as a second lieutenant in military intelligence in 1981. His military assignments included multiple tours at Fort Bragg, North Carolina, with the 82nd Airborne Division, XVIII Airborne Corps, and Joint Special Operations Command, where he deployed for the invasion of Grenada and Operation Uphold Democracy in Haiti. He also served with the 25th Infantry Division at Schofield Barracks, Hawaii, at the Joint Readiness Training Center at Fort Polk, Louisiana, and the Army Intelligence Center at Fort Huachuca, Arizona.