The National Archaeological Museum was founded by presidential decree on August 9, 1893 (Greek Government Journal I, 152, 'On the organization of the National Archaeological Museum'). Its purpose was 'the study and teaching of the science of archaeology, the propagation of archaeological knowledge and the cultivation of a love for the Fine Arts'. Its collections were segregated into: Sculpture, Vases, Clay and Bronze Figurines and other Ancient Figurines made of various materials, Inscriptions, which later went to the Epigraphic Museum, Pre-Hellenic (the Mycenaean collection), and Egyptian. The museum was also equipped with conservation laboratories and a cast workshop.

With the declaration of the Second World War in 1939, the museum's antiquities were stored for safety in the museum itself, the vaults in the Bank of Greece and in natural grottos. At the end of the war, the museum's director Christos Karouzos undertook the re-exposition of the exhibits and the architect P. Karantinos remodeled the exhibition spaces. During that time the temporary display was limited to ten rooms of the east wing. Christos and Semni Karouzou completed the re-exposition in 1964, having created an exemplary display of the development of ancient Greek art from prehistory to the Roman period. The unique Greek collection of Egyptian antiquities was exhibited for the first time thirty years later, in 1994.