Schaeffer graduated in 1971 from Washington University in St. Louis with a bachelor's degree in anthropology. She earned a master's degree in urban studies from the University of Chicago in 1974, with a master's thesis on Islam and the City: A Research Ideology Reassessed supervised by geographer Paul Wheatley. She returned to the University of Chicago for doctoral studies, completing a Ph.D. in sociology there in 1984. Her dissertation, Distress in Major Adult Roles and Depression among White Men and Women, was supervised by Edward O. Laumann.
