Bowen earned his B.S. in 1934 at the University of Tennessee in Knoxville. He received his MD in 1937 at the Medical School of the University of Tennessee in Memphis. After that, he had internships at Bellevue Hospital in New York City in 1938 and at the Grasslands Hospital, Valhalla, New York, from 1939 to 1941. From 1941 to 1946, he did his military training followed by five years of active duty with Army in the United States and Europe. During the war, while working with soldiers, his interest changed from surgery to psychiatry. Though he had been accepted for a post-military fellowship in surgery at the Mayo Clinic, in 1946 he started at the Menninger Foundation in Topeka, Kansas, as a fellow in psychiatry and personal psychoanalysis. This psychiatric training and experience lasted until 1954.