Behnken was born in St. Ann, Missouri on July 28, 1970. After graduating from Pattonville High School in Maryland Heights, Missouri, he attended Washington University in St. Louis where he majored in mechanical engineering and physics and was a member of the Air Force Reserve Officers' Training Corps. He then went to California Institute of Technology (Caltech) in Pasadena, California for graduate school, where he earned master's and doctorate degrees in mechanical engineering. 