The Auberge de Provence was opened as the National Museum in 1958 by Agatha Barbara, then the Minister of Education. The museum originally included the archaeological collection on the ground floor and fine arts on the first floor. The first curator was Captain Charles G. Zammit, the son of the eminent Maltese archaeologist Sir Themistocles Zammit.
In 1974, the fine arts collection was moved to the National Museum of Fine Arts, newly established in the Admiralty House building in South Street, Valletta, and the National Museum was renamed the National Museum for Archaeology.
The museum was refurbished and upgraded in 1998. Artifacts were placed in climate-controlled displays so that the exhibition met with current conservation standards.