Cowan was born in Sacramento, California. He enlisted in the United States Navy at the age of 17, received an appointment to and graduated from the U.S. Naval Academy in 1966, and was commissioned as a lieutenant the United States Marine Corps. He subsequently spent three and a half years in Vietnam. On his first tour he served as a platoon commander with the 3rd Battalion, 26th Marines, along the DMZ and at the siege of Khe Sanh, and later was in charge of the 3rd Marine Division's Kit Carson Scouts program for five months. From 1969 onwards, he was advisor for the South Vietnam military in the Rung Sat Special Zone for two and a half years. Most of that time was spent with small units and getting experience of raids, ambushes, riverine operations and intelligence gathering with the Central Intelligence Agency. During his last year he led the Rung Sat's Provincial Reconnaissance Unit. He received numerous awards for valor in combat and was wounded three times.