Flynn studied at public and parochial schools, La Salle Academy, Fordham Law School, and the Massachusetts Institute of Technology, studying military aeronautics in the latter school. In 1916, he served with the 69th Regiment at the Mexican border. In 1917, during World War I, he sailed for France. He was then sent to Foggia, Italy, resuming air training in a camp surpervised by future New York City Mayor Fiorello La Guardia, at the time a captain. He then returned to France and was assigned to the 28th Squadron of the Second Pursuit Group. He saw service in the front. On Armistice Day, his plane was shot down near the American lines. He was rescued unharmed and informed the armistice was declared. He held the rank of First Lieutenant in the American Air Service, Flying Officer.