Although there are records of Maltese personnel manning the site as far back as 1417, the actual fort was built by the Knights of St. John of Jerusalem in 1552, with an impending Ottoman Turk invasion in mind. It was constructed on the design of Pietro Pardo, and had the aim of guarding the entrances to the two harbours on either side of Mount Sceberras peninsula.

Fort St. Elmo had the shape of a four pointed-star, with a cavalier protecting it from the seaward side and one ravelin offering protection from land. When the feared invasion did take place in 1565, the stage was set for one of the most glorious, though tragic, moments of Maltese military history. The Turks realised that to secure safe anchorage for their fleet in either of the two harbours flanking the peninsula, they would first have to neutralize Fort St. Elmo.

They therefore launched a massive and desperate attack on this outpost, including a continuous bombardment from the heights of Mount Sceberras. On June 23, 1565, the 600 or so defenders of the Fort fell to the last man, as they were overcome by the vast Turkish hordes, following a month-long siege.

With the end of the Great Siege, Fort St. Elmo was restored and during the course of the seventeenth century, a new enceinte was constructed around the Fort, thereby connecting it to the new city of Valletta. It was at this Fort that Malta's involvement in the Second World War registered its first victims, during a bombing raid effected on the day after Italy declared war, on 11 June 1940.

In July 1941, the Fort was again on centre-stage when its Maltese defenders proved instrumental in the repulsion of an Italian E-Boat attack on a recently-arrived convoy in Grand Harbour. Fort St. Elmo's vigilant days are now over, and the upper part of the Fort is today utilised by the Malta Police Force as a Police Academy.

The lower part owes its more recent fame as the site for the shooting of the film "Midnight Express". Fort St. Elmo is open to the public by the kind permission of the Commandant of the Police Academy.