When the island was under Aragonese Rule, this building was known as Caste/lo a Mare - the Castle by the Sea. It is believed that in Phoenician times there stood a temple dedicated to Asthart and later, under Roman domination, to the goddess Juno. The original stronghold may date from the 11th century when the island was under Arab occupation. From the 14th century onwards, under Aragonese rule, the fort was the home of the powerful Nava family, feudal lords of the island.

Up to 1400, the fort had only 3 small guns and several mortars. After 1570, the Knights added a cavalier tower. During the siege of 1565, the fort was the headquarters of Grand Master La Valette. For some time during the rule of Grand Master La Cassiere, the fort was used as a jail to imprison rebellious knights.

There are two chapels inside the fortress - one dedicated to the Virgin (12th century) and one to St. Anne (1534). The Grand Masters who died before Valletta was built were buried in the latter chapel, and their remains were later transferred to St. John's Cathedral. Many defenders who fell during the siege are also buried in the fort. The British turned St. Angelo into Naval Headquarters and named the Fort, H.M.S. St. Angelo.

Several famous admirals, including Lord Mountbatten, were stationed there. During World War II the Fort was the Headquarters for Naval operations in the Mediterranean. Part of the Fort has now been leased to the Order of St. John of Jerusalem, Rhodes and Malta and extensive restoration works are in hand.

It is intended to use this part of the Fort for the holding of meetings between different members of the Order coming from all parts of the world. Such meetings are held both for spiritual purposes as well as for the establishment of mutual help between the different national associations in the field of assistance to the handicapped, the sick, the poor and the elderly. Part of the premises will eventually be turned into a museum.