A small collection of artefacts grew out of the very fruitful archaeological research in Boiotia at the beginning of the twentieth century. Antonios Keramopoullos founded the Archaeological Museum in 1905. It was housed in a two-storey building, which was specially built on the projection at the north end of the historic acropolis of the Kadmeion. Apart from the sculptures of Thespiai and Ptoo and other surface finds from Boiotia, the museum displayed the finds from Keramopoullos' investigations in the palace of Kadmos, those from the Polyandrion at Thespiai, and many more from the Mycenaean and Classical cemeteries of Thebes, Tanagra and Ritsona, and from the prehistoric settlement of Eutresis.

The old replete museum was replaced by a new one built on the same location. This new museum, the life's work of the then Ephor of Antiquities, I. Threpsiadis, was inaugurated in 1962 and housed many new finds, particularly those from the sanctuary of Artemis at Aulis. During the 1960's the collection was enriched by finds from the important excavations at the Kadmeion, by several representative objects from the German excavations at Kabireion and from the excavations at Thebes, Orchomenos and Tanagra, which were conducted by the Ninth Ephorate of Prehistoric and Classical Antiquities. During this same decade the museum's garden was used for the first time to display antiquities, while the finds from the Mycenaean cemetery at Tanagra were exhibited in a special room which opened to the public in 1972.

The spectacular archaeological discoveries in the centre of the Kadmeion on the Mycenaean and Classical acropolis of Thebes, the extensive cemeteries of Akraiphnion, the many rescue excavations and random finds in settlements, cemeteries and sanctuaries in Boiotia and in the Larymna region, increased the number of finds and made the construction of a new museum building at the west of the promontory necessary. At the same time a much-needed parking area was created east of Keramopoullos Square and the Medieval tower.