Prior to the arrival of the Knights of Malta in 1530, a watchtower existed on this point. Reinforcement of this strategic site commenced in 1533. After the Dragut Raid of 1551, during which the Turks sail unopposed into Marsamxett Harbour, work commenced on a major expansion, and by the time of the Ottoman Siege of Malta in 1565, this fortification had been reinforced and extended into a modest star fort.
Fort Saint Elmo was the scene of some of the most intense fighting of the 1565 siege, and it withstood massive bombardment from Turkish cannon deployed on Mount Sciberras that overlooked the fort and from batteries on the north arm of Marsamextt Harbour, the present site of Fort Tigne. The initial garrison of the fort was around one hundred knights and seven hundred soldiers, including around four hundred Italian troops and sixty armed galley slaves. The garrison could be reinforced by boat from the forts across the Grand Harbour at Birgu and Senglea.
During the bombardment of the fort, a cannon shot from Fort St Angelo across the Grand Harbour struck the ground close to the Turkish battery. Debris from the impact mortally injured the corsair and Ottoman admiral Dragut Rais, one of the most competent of the Ottoman commanders. The fort withstood the siege for over a month, falling to the Turks on 23 June 1565. None of the defending knights survived, and only nine of the Maltese defenders survived by swimming across to Fort St. Angelo on the other side of the Grand Harbour after Fort St Elmo fell.
Though the fort was reduced to rubble during the bombardments, when the Ottomans abandoned the siege the fort was rebuilt and reinforced, becoming partially incorporated into the seaward bastion of the fortress city of Valletta.
The original George Cross that was awarded to Malta by King George VI in April 1942, is on display in the National War Museum, which occupies part of the Fort.
Now home to the Malta Police Academy, parts of this 16th-century fort on the tip of the Valletta peninsula have appeared in two swashbuckling adventure movies, Cutthroat Island and The Count of Monte Cristo (doubling for Marseille), as well as the forthcoming 1960s espionage drama A Different Loyalty, in which the fort doubled for a Beirut street market, and Midnight Express, which used the fort’s disused barracks to represent a Turkish prison.