Michael Phayer (born 1935) is an American historian and professor emeritus at Marquette University in Milwaukee and has written on 19th- and 20th-century European history and the Holocaust.

Phayer received his PhD from the University of Munich in 1968 and joined Marquette's Department of History in 1970. He became Professor in 1990 and retired in 2002. He is the Ida E. King Distinguished Visiting Scholar of Holocaust Studies at Stockton University. He has published numerous research articles and books relating to Nazi Germany, the Holocaust and the Catholic Church, including his most recent, Pius XII, the Holocaust, and the Cold War (2007). His previous work was The Catholic Church and the Holocaust, 1930–1965 (published in 2000).