Following the negotiation of the Treaty of the Pyrenees in 1659, the Fort de Bellegarde in Le Perthus passed from Spain into the hands of the French state. That bastion had been the border defense for Spain, so to replace it and stop possible future invasions, it was decided to build a fortress on the hill in Figueres. The first stone was placed on December 13, 1753. The name of Sant Ferran (San Fernando in Spanish) was given in honor of King Ferdinand VI of Spain.

Early in the Peninsular War with France that began in 1808, the castle was captured by the French. On 9 January 1810, Mariano Álvarez de Castro, hero of the recent third siege of Girona, was brought to Sant Ferran from Perpignan to be imprisoned.[1] The following day he was found dead, of a fever, according to the French, poisoned, according to the Spanish. He was buried, wrapped in only a sheet, in the cemetery there. In 1815 a black marble tablet was placed on his grave which stated that Álvarez had been poisoned, and was a Victim of the Iniquity of the French Tyrant. In December 1823 French troops, ironically intervened Spain in order to help restore the Bourbon throne of Ferdinand VII, passed through Figueres, and on the orders of Marshal Moncey, formerly Napoleon's Inspector-General of Police, destroyed the plaque.[1] The French had surrendered the fort in June 1814, the last French fort to surrender in the Peninsular War.

On Feb. 1, 1939, Juan Negrín, last prime minister of the Second Spanish Republic, convened in the castle the final meeting on Spanish soil of the Republican Spanish Cortes. A week later, the fortress fell to the forces of Francisco Franco.

From May 1940 to December 1942, Francoist regime used the castle as a concentration camp where returned republicans from France were held. Thousands of prisoners were interned there, most of them to be distributed to other camps.[2]