The Department of Prehistory was established in the early 1950-es together with the other two early established departments, the Departments of Classic and Mediaeval Archaeology after the Institute and the Museum were united within the BAS. Prof. Vassil Mikov was the first head of the Department. Prof. G. I. Georgiev, an outstanding specialist on the late prehistoric periods, known all over Europe, was head of the Department from 1965 to 1982. Dr. Rumen Katincharov, Senior Research Fellow, a specialist on the Bronze Age, headed the Department from 1982 to 1989. In the following 10 years (1989-1999) Prof. Dr. Habil. Vassil Nikolov, a specialist on the Neolithic and Chalcolithic in southeast Europe headed the Department of Prehistory. Dr. Ivan Gatsov, Senior Research Fellow, a specialist on the flint tools of the late prehistoric periods in the Balkans, was head of the Department for a short time (1999-2000) and after that the position was taken by Dr. Nikolai Sirakov, Senior Research Fellow, a specialist on the Paleolithic in the Balkans. Since 2003, Dr. Maria Gurova, Senior Research Fellow, has been the head of the Department; she is a specialist on use-wear analysis of flint artifacts from the later prehistoric periods.

The Department of Prehistory takes decisions on basic organizational issues. Its main function is the scholarly debate and the acceptance of academic papers/research, appointment of PhD students and evaluation of PhD thesis, nominations for scientific degrees. Administratively, the Department of Prehistory at the Institute of Archaeology and Museum is the sole body taking decisions and discussing proposals for archaeological excavations of prehistory specialists in the country.