Payton transferred to the University of Wisconsin–Madison for her M.S. degree in clinical psychology in 1948. Under the "separate-but-equal" doctrine, the state of Virginia covered her expenses at the out-of-state school because she pursued a graduate degree in a discipline available to White students at a White state schools, but unavailable to Blacks at a Black state school. Payton conducted her masters thesis on the then newly developed Wechsler-Bellevue Test of Intelligence and concluded that the test provided an inaccurate measure of the true ability of Blacks.