The Auberge de Provence was built in 1571 to house the knights of the Order of Saint John from the langue of Provence. It was designed by the Maltese architect Girolamo Cassar, who directed the building of most of the important buildings in the early days of Valletta. The building featured Mannerist characteristics usually associated with Cassar.
The Grand Salon on the first floor is the most ornate room in the building. The Knights used it for business discussions, and as a refectory and banqueting hall, where they sat at long tables according to seniority.
When Napoleon expelled the Knights from Malta in 1798 the Auberge was leased to the Malta Union Club. The Auberge de Provence was opened as the National Museum in 1958 by Agatha Barbara, then 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, then 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.