Born and raised in Prague, Czechoslovakia, Bauer was fluent at an early age in the Czech, Slovak and German languages, later learning Hebrew, Yiddish, English, French and Polish. His father had strong Zionist convictions and during the 1930s he tried to raise money to get his family into the British Mandate of Palestine. On March 15, 1939, the family migrated to Palestine.
Bauer attended high school in Haifa and at sixteen, inspired by his history teacher, Rachel Krulik, decided to dedicate himself to studying history. Upon completing high school, he joined the Palmach. He attended Cardiff University, Wales on a British scholarship, interrupting his studies to fight in the 1948 War of Indepedence, after which he completed his degree.
Bauer returned to Israel to join Kibbutz Shoval and began his graduate work in history at Hebrew University. He received his doctorate in 1960 for a thesis on the British Mandate of Palestine. The following year, he began teaching at the Institute for Contemporary Jewry at the Hebrew University. He served on the central committee of Mapam, then the junior partner party of Israel's ruling Mapai (Israel Labor Party), and was a visiting professor at Brandeis University, Yale University, Richard Stockton College, and Clark University. He was the founding editor of the Journal for Holocaust and Genocide Studies, and served on the editorial board of the Encyclopaedia of the Holocaust, published by Yad Vashem in 1990.
In recent years, Bauer has received recognition for his work in the field of Holocaust studies and the prevention of genocide. In 1998, he was the recipient of the Israel Prize, the highest civilian award in Israel. In 2001, he was elected a Member of the Israeli Academy of Science. Currently, he serves as academic adviser to Yad Vashem, academic adviser to the International Task Force for Holocaust Education, Remembrance, and Research, and senior adviser to the Swedish Government on the International Forum on Genocide Prevention.
Bauer is a respected authority on the subjects of the Holocaust, anti-Semitism and the Jewish resistance movement during the Holocaust. In Bauer's view, resistance to the Nazis comprised not only physical opposition, but any activity that gave the Jewish people dignity and humanity in the most humiliating and inhumane conditions. Furthermore, Bauer has disputed the popular view that most Jews went to their deaths passively—"like sheep to the slaughter." He argues that, given the conditions in which the Jews of Eastern Europe had to live under and endure, what is surprising is not how little resistance there was, but rather how much.
Bauer has often criticized what he considers to be deleterious trends in writing about the Holocaust. He has often taken exception to those who argue that the Holocaust was just another genocide. Though he agrees that there have been other genocides in history that have targeted groups other than Jews, he argues that the Holocaust was the worst single case of genocide in history, in which every member of a nation was selected for annihilation, and that it therefore holds a special place in human history.
Yehuda Bauer is currently a Professor of Holocaust Studies at the Avraham Harman Institute of Contemporary Jewry at the Hebrew University of Jerusalem.