Schaefer majored in earth and planetary sciences at Washington University in St. Louis, where she earned a bachelor's degree in 2002. She continued to work at Washington University until 2011, when she became a graduate student in astronomy at Harvard University. She completed her Ph.D. in 2016, under the supervision of Dimitar Sasselov; her dissertation was The Atmosphere-Interior Connection: Rocky Planets as Linked Chemical Systems.
