The National Archaeological Museum was founded at the end of the nineteenth century to house and safeguard antiquities from all over Greece and to promote their historical, academic and artistic value to the world. The first Greek archaeological museum was established in 1829 by Prime Minister I. Kapodistrias and housed in the Aigina Orphanage. However, the transfer of the nation's capital from Nauplion to Athens and the increasing number of archaeological discoveries during the subsequent decades necessitated the creation of a purpose built archaeological museum in the new capital. Several plans and locations were proposed by Greek and foreign architects who were working on the reconstruction of Athens. The plans of L. Lange and P. Kalkos were approved and the museum was built on a plot donated by Eleni Tositsa. E. Ziller did the final landscaping. The Greek state, the Archaeological Society and Nikolaos Vernardakis, a wealthy expatriate in Russia, financed the project. The core of the building was completed in 1889; the east wing was added in 1903-1906, and architect G. Nomikos appended a two-storey annex on the east side of the main building in 1932-1939.

The transfer of antiquities to the museum began in 1874, after the completion of the west wing and during the construction of the central core. The most important finds from Greece had already been transferred to the museum by the time the main building was completed in 1889. The antiquities of the Archaeological Society were handed over by 1893. The collections were also enriched by important donations at this time, such as that of the Egyptian Collection of Ioannis Dimitriou in 1890.

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.