Ernst Klee was born in Frankfurt, Germany. He l eft school early and worked as an apprentice plumber before deciding to study for the Arbitur (university entrance examination). He took courses in Protestant theology and social work at Frankfurt Technical College, where he later taught courses on education for disabled people. He became a journalist for the weekly Die Zeit, and later was a freelancer. He wrote numerous articles and books, specializing in socially-excluded groups such as the homeless, psychiatric patients and the disabled. He also wrote extensively on German history. He was best known for exposing and documenting the role of German medical and social work professionals in the mass murder of the disabled, mentally ill and disadvantaged people during the Nazi era, a topic that academic historians had ignored. His books included The Good Old Days: The Holocaust Through the Eyes of the Perpetrators and Bystanders (1988, English translation published 1991). In 1997, Klee received the Geschwister-Scholl-Preis for his book, Auschwitz, die NS-Medizin und ihre Opfer (Auschwitz, Nazi Medicine and Their Victims), and he won the Goethe Medal for his book Deutsche Medizin im Dritten Reich: Karrieren vor und nach 1945 (German Medicine in the Third Reich: Careers Before and After 1945).
A school for disabled people in Mettingen was renamed in his honor in 2005.