Stein received her undergraduate B.A. in Biological Basis of Behavior from the University of Pennsylvania, a M.S. degree from Hood College in Biomedical Science and a Ph.D. from the University of New Mexico in Biomedical Science. Stein completed her first post-doctoral fellowship in the intracellular trafficking laboratory of Dr. Angela Wandinger-Ness at UNM and a second fellowship in intracellular pathogen trafficking at Yale in the laboratory of Dr. Craig Roy.