Erected by Portuguese navigators in the 19th century (1838–1844), on what was then known as Morro da Ponta Negra, the structure has served as the Namibe Naval Base (BNN) since 1991.

It dates back to the first half of the 19th century, within the context of the Portuguese colonization of the Bay of Namibe, with the function of defending the presídio (a military colonial settlement) founded there.
After studies of the coastline and the hinterlands of the region, initiated in 1839, the then Governor-General of the Province of Angola, Manuel Eleutério Malheiro, ordered in February 1840 the construction of a fort in the Bay of Moçâmedes, at a time when its military occupation was beginning.
This fortification was completed in 1844, officially receiving the designation Fort of São Fernando by Official Letter No. 249, dated June 12, 1849, from the Governor-General to the Ministry of Overseas Territories in Lisbon. In this way, homage was paid to Ferdinand II of Portugal, husband of Queen D. Maria II (1826–1828; 1834–1853).

Its first commander was Artillery Lieutenant João Francisco Garcia (1840–1845). The first civilian settlers of Moçâmedes were two groups of Portuguese who withdrew from the Province of Pernambuco, in Brazil, during the Praieira Revolt (1848–1850), in 1849.
In the 20th century, its facilities were occupied by the District Command of the Public Security Police, until the country’s independence.
With independence, on November 11, 1975, the former District of Moçâmedes became the Province of Namibe.
The Fortress of Moçâmedes is a site of historical and tourist interest. Although it may not be in perfect condition due to the wear of time, it represents an important landmark of Angola’s historical and cultural heritage.

Today, the fort is occupied by the command of the Namibe Naval Base of the Angolan Navy.