With the support of the politician Bernardino Machado, a legal decree for the creation of a National Ethnographic Museum was established on 20 December 1893.

The museum's metalwork collection is representative of the mineral and metallurgical history of the Iberian Peninsula, which includes tools created in copper from the Chalcolithic period (middle of the 3rd century BC).

Of particular importance are a group of artefacts named the "Atlantic bronzes" and farming tools from the Roman Period.The museum also has the largest collection of Classical sculpture in Portugal.

From this period, items of particular technical and stylistic value are the toga-draped statues from Mertola, Apollo from the Herdade do Álamo (Alcoutim) and the sarcophagi from Tróia and Castanheira do Ribatejo.

Emblematic of the Celtic period in North-eastern Portugal are the monumental granite statues representing princes or noblepeople, often referred to as the "Gallecian Warriors" which guard the museum's entrance.

Nevertheless, within this collection, the most important items are mosaics from the Roman Villas of Torre da Palma, Santa Vitória do Ameixal, Milreu and Montinho das Laranjeiras.

The museum's collection, built over more than half a century, has over 1,000 items of gold jewellery dating from pre-history to ancient history.

Some of the most important items found in this collection are the treasures of the Herdade do Álamo and Baião, the Arrecadas from Paços de Ferreira and the notable torc of Vilas-Boas.

The museum also holds a notable collection of votives to an indigenous divinity from the Endovelicus period located in the Sanctuary of São Miguel da Mota.

Although in lesser numbers, there are also honorific epigraphs, which, amongst others, include the Civitas Ammaiensis to Emperor Claudius (part of his imperial cult).

From the late Roman period, a 3rd-century AD collection was found in Porto Carro and from the 4th century AD a collection was found in Tróia.The fragile and difficult nature of preserving organic materials led to the development of special storage facilities in the museum, where such materials could be stored in a controlled environment.

Of particular note are the collections of popular religious art, which contain religious iconography, votive offerings, votive panels and amulets; pastoral arts (spoons, horns, gunpowder horns); items with keys; musical instruments (including an 18th-century accordion) toys; smoking paraphernalia; Portuguese faience from the 17th to 20th centuries from several factories and periods; and pottery from Barcelos, Gaia, Caldas da Rainha, Mafra, Nisa, Estremoz, Redondo and the Algarve.

Archaeological sites in Mértola, Castro Marim, Torre de Ares and Troia have revealed commercial ties between the eastern and western Mediterranean and the north of Africa through the import of the famous Baetic olive oil and wine, found in amphorae of types Dressel 20, Dressel 14, Haltern 70 and Africana I and II.

The National Museum of Archaeology was originally based in Lisbon's Academy of Sciences in room provided by the Geological Commission.

[12] To overcome the physical limitations of its facilities, it was suggested in the 1950s that the museum move part of its collection to the Lisbon University campus.