Stephan received his BSc in Biochemistry and  PhD in Immunology from the University of Bristol, UK. Following postdoctoral work at the Dana-Farber Cancer Institute in Boston and at the Massachusetts Institute of Technology in Cambridge, MA, Stephan became a group leader at the Rudolf Virchow Center at the University of Wurzburg, Germany, in 2007. In 2012, Stephan returned to Boston to join the section for Immunobiology at the Joslin Diabetes Center, where his lab continues to study autoimmunity with a focus on type 1 diabetes.

Stephan is Associate Professor in Department of Medicine at Harvard Medical School, a Faculty Member of the Harvard Program in Immunology, a Principal Faculty Member of the Harvard Stem Cell Institute (HSCI), the Director of the Mouse Genome Editing core facility and Director of the Fellows Affairs Council at Joslin Diabetes Center, and Leader of the Diabetes Program at HSCI.