 After he completed his military service, he coached for two years at University of Kansas, he compiled a 15–3–2 (.786) record, winning the conference title in each season.After he left Kansas, Sauer coached at the United States Naval Academy (1948–1949), and Baylor University (1950–1955), compiling a career college football record of 78–55–9 and earning trips to both the Orange Bowl and the Gator Bowl.Sauer remained at Baylor as Athletic Director until 1960 when he became the first General Manager of the New York Titans of the American Football League.