The foundation of the museum was made possible through the support of politician Bernardino Machado, leading to the establishment of a National Ethnographic Museum. Officially opened in 1906, the museum is built in the Neo-Manueline style, reflecting the architectural heritage of Portugal. Its location within the Jeronimos Monastery adds to its historical and cultural significance.

The National Museum of Archaeology serves as a center for archaeological research in Portugal and has received international recognition for its contributions to the field. The museum has been awarded the prestigious Genio Protector da Colonia Augusta Emerita prize, presented by the Foundation for Roman Studies and the Friends of the National Museum of Roman Art in Mérida, Spain.

Situated in Santa Maria de Belém, the museum occupies a substantial portion of the Mosteiro dos Jerónimos, facing the Praça do Império. This area is highly frequented by tourists due to the presence of numerous museums and heritage sites.

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Over the years, the museum has undergone various reorganizations to accommodate its expanding collection. Initially, it was housed in Lisbon's Academy of Sciences before relocating to the Mosteiro dos Jerónimos in 1903. As the museum became the primary repository for archaeological finds in the country, its collection grew significantly. To address the limitations of its facilities, proposals were made to relocate a portion of the collection to the Lisbon University campus or the Cordoaria Nacional.

The mission of the National Museum of Archaeology, initially envisioned by José Leite de Vasconcelos, is to present the history of the Portuguese people from their origins to the formation of the nation. It has been an important platform for archaeological research, with ongoing excavations contributing to the museum's collection. In addition to research and education, the museum serves as a national repository and exhibition space for archaeological artifacts. Since 1895, it has published the periodical Portuguese Archaeologist.

Today, the National Museum of Archaeology continues to preserve and showcase the rich archaeological heritage of Portugal. With its extensive collection, it provides visitors with insights into the country's ancient past and the evolution of its people. The museum stands as a testament to the vision of its founder and the ongoing commitment to archaeological research and education in Portugal.