The City of Prague Museum’s Department of Archaeology was established in 1941 as Abteilung für Vor- und Frühgeschichte by taking over and annexing the previously independent Jíra Archaeological Museum at Hanspaulka in Prague – Dejvice, which was administered by the Association for the Preservation and Expansion of J. A Jíra’s Archaeological Collections. Because the annex was accompanied by a strong enforcement by the German-controlled Education Department of the City of Prague and L. Zotz, the head of the Institute of Prehistory and Early History at the German Charles University, the annex formally repeated between 1945 and 1946 – the archaeological department was called the Department of Prehistory of J. A. Jíra. After the mid-1950s, the department was dissolved and transferred, as a subdivision of archaeology, into the newly established Specialized Department of the City of Prague Museum, which included divisions of history and collection care. On January 1, 1975, the Department of Archaeology of the City of Prague was established, which, during the next museum reorganization in 2004, was renamed the Department of Archaeological Collections of the City of Prague Museum.
The Department of Archaeology had its seat at the Hanspaulka Chateau in Prague – Dejvice from the day it was established. In 1995, it moved to the former precincts of Koh-i-noor Company in Prague – Stodůlky where a new central division of the museum began to be formed shortly before. As early as the second half of the 1940s, the Department of Archaeology joined in systematic and rescue terrain research in Prague and vicinity. The large research in Prague neighbourhoods such as Hloubětín, Kobylisy, and Čakovice in the 1950s (B. Soudský), future research of the uphill estates of Baba in Prague – Dejvice and Klobouček in Prague – Zličín (J. Havel), rescue research prior to the building of the South-West housing estates in Prague – Stodůlky, and the retention reservoirs in Jiviny near Prague – Ruzyně in the 1970s and 1980s (J. Kovářík) were especially valuable. In 2006, the terrain research was considerably limited; today, the Department of Archaeology participates only in smaller scope events in the city centre because it mainly focuses on the evaluation of the acquired collection of resources and systematic processing of the so-called old archaeological collection.
The large archaeological collection administered by the department is the foundation of the permanent museum expositions Prague in Prehistory and Prague in the Middle Ages. Since the 1960s, the department of archaeology has prepared temporary exhibitions as well such as Archaeologic Programs for Schools for schools and interest groups and Archaeologic Programs for Public for the larger public.
The professional activities of the department employees (archaeological research, processing of the so-called old archaeological collection, history of Prague archaeology) are widely presented in Archaeologica Pragensia magazine. The City of Prague Museum edition Acta Musei Pragensis has published several monographs on archaeological themes.