The Prague City Museum's Department of Archaeology was established during World War II, in 1941, by taking over and annexing the previously independent Jíra Archaeological Museum at Hanspaulka in Prague – Dejvice, which had been managed by the Association for the Preservation and Expansion of J.A. Jíra's Archaeological Collections. The Hanspaulka Palace became the seat of the new department. During 1945–1946, the Department of Archaeology was renamed Department of Prehistory of J.A. Jíra. In the 1950s, the department was dissolved and in the next decade turned into a subdivision of archaeology of the newly established specialised museum department that included divisions of history and collection care. At the beginning of 1975, a new independent Department of Archaeology was established, renamed the Department of Archaeological Collections in 2004. After leaving the Hanspaulka Palace in 1995, the department moved to the museum's building in the former Koh-i-noor company compound at Prague – Stodůlky.
The Prague City Museum's rescue archaeological research during the construction of the Sladovna Podbaba residential compound, Prague-Dejvice in 2004, photo by M. Kostka, MMP.
After the mid-1940s, the department became fully involved in systematic and later rescue archaeological research in Prague. In 2006, the terrain activities were significantly reduced, putting focus on the Prague Heritage Area and its immediate vicinity. The department employees have mainly been pursuing the processing of sources and their presentation since then.
The Department of Archaeological Collections of the Prague City Museum currently has more than 800,000 inventory numbers but the number of objects is much higher. The collections' beginnings are associated with Josef Břetislav Jelínek (1843–1926), an amateur archaeologist, the first custodian, and from 1895 the first director of the Municipal Museum of Prague. The collection of Josef Antonín Jíra (1868–1930) is its most valuable part; assembled between the end of the 19th century and 1912, it was displayed in the Jíra Archaeological Museum at the Hanspaulka Palace in Prague – Dejvice. The collection was acquired by the Municipal Museum of Prague in 1941 as a new department of archaeology.
After the mid-1940s, the collection has been growing especially thanks to museum's terrain research. Since 2005, non-state archaeological institutions in Prague have substantially been contributing to it, as based on the law they provide the Prague City Museum with findings from their archaeological research.
The collections further include various documents, including photo archives, related to the Prague City Museum's archaeology and the collection fonds from the late 19th century. The collection and its documents are available to researchers only at the museum under the terms and conditions of the Prague City Museum.