Bowen received his elementary and high school education from local schools and went on to graduate from Indiana University Bloomington with an A.B. in 1939 and the Indiana University School of Medicine with an M.D. in 1942. At IU, he became a member of the Delta Chi fraternity as well as the Phi Beta Pi medical fraternity. He holds 30 honorary degrees including those from schools in his home state such as Indiana University, the University of Notre Dame, Ball State University, Valparaiso University, and Anderson University. In addition to an honorary degree, Bethel College also named their campus library in his honor.