He began his flying career after graduating from the Hellenic Air Force Academy in 1986. After completing his basic pilot training, he began piloting the F-5A. He transitioned to the F-16 and was subsequently assigned to 330 Mira of the 111th FW at Anchialos AB in central Greece. The 330th, the first Greek unit to receive the F-16, performs air-defense missions. Vagenas uses his vast F-16 experience to instruct new F-16 pilots at Anchialos.