Shaffer received his master's degree from Teachers College, Columbia University, in 1940. He then enrolled in the doctoral program at New York University, from which he received the Ph.D. degree in 1945. He met Marjorie Jane Fitch at the International House in New York City and they married in 1940. In 1941 Shaffer took his first student affairs position as an assistant to the Dean of the School of Business at Indiana University.
