A reference in 1360 statutes of the Prague university is commonly believed to be the first testimony to the existence of a university archive in Prague. A central (rectorial) archive kept documents, especially deeds and charters, attesting to the legal status and properties belonging to the university. The first list of the university’s documents was made, probably for reasons of property administration, in mid-1540s. After the Battle at the White Mountain, the ‘fiscus’ (university treasury) was together with charters of privileges and other archival materials sealed and in the following year handed over to Jesuits residing in the nearby Clementinum. An important turning point in the history of the Prague university archive came with the Theresian reforms, when an imperial rescript of 1755 specified how the university is supposed to proceed in managing its archival materials. For a long time afterwards, the archive was managed by the university syndic T. A. Putzlacher. In early 1820s, most of the hitherto fragmented parts of the archive were merged and moved to a room on the Carolinum ground floor.

After the split of the Prague university into a Czech and a German university in 1882, the university archive was managed by the German university, while the Czech one was granted the right of ‘full and equal use’. Adolf Bachmann, professor of history, was appointed university archivist and it was Bachman who at this time made a new inventory of the archival material in his care.

‘The issue of the archive’ remained a point of contention in the not fully resolved relation between the Czech and the German university even after the archive was handed to the care of the Czech university on 29 October 1918. In 1934, the start of work on the reconstruction of the Carolinum was the reason why the archive was moved to facilities in the new building of the Faculty of Law of the Charles University. After the occupation of the Czech Lands by Nazi Germany in 1939, the university archive was once again entrusted to the care of the German University. At the end of the war, a relatively large amount of archival materials was lost: it was removed during the evacuation of the German University in Prague and remains missing until this day.

In May 1945, Prof. Václav Vojtíšek was appointed head of the university archive. The Institute of the History of Charles University, a scientific institute focusing on the research of history of Charles University, was founded in 1958. In late 1960s, the archive moved from provisory facilities in the building of the Faculty of Law into a reconstructed building within the Carolinum compound, where it resides until today. In 1970, the Institute of the History of Charles University was after a previous intervention of the State Security abolished and transformed into the Archive of Charles University, which, however, had lost the status of a scientific institution. After the fall of the Communist regime, a scientific institute researching the history of the Charles University was reinstated and since that time, the university archive is one of the two departments of the Institute of the History of Charles University and Archive of Charles University.