The castle is one of the "Five Sons of Carcassonne" along with the castles Quéribus, Puilaurens, Termes, and Aguilar, all situated atop 'unassailable' rocky peaks. It is called 'Celestial Carcassonne' because it is the biggest of the five castles and it is as vast as Carcassonne.[1]

The site was occupied during Roman times from the beginning of the 1st century B.C., as recent archaeological excavations have shown. The first historical references to the castle appeared in 806. It was then Catalan and was called Perapertusès. It belonged to the Count of Besalú, a small city situated in Catalonia between Figueres and Olot according to a text from 1020.

It then passed into the earldom of Barcelona in 1111, and then into the viscountcy of Narbonne. From 1180, the Count of Barcelona (Alphonse II, who later became the king of Aragon) secured his independence from vassalage to the king of France. The area became a de facto border.

At the time of the Albigensian Crusade, it was the fief of Guillaume de Peyrepertuse who, not wanting to submit, was excommunicated in 1224. He did finally submit after the failure of the siege of Carcassonne, and the castle became a French possession in 1240. In 1242, Saint-Louis decided to reinforce it and add a second part, the Sant Jordi dungeon, located higher up on the ridge. The Sant Jordi dungeon was then constructed in 1250-51 and the Old Dungeon as well as the Sainte-Marie Church were re-purposed. The situation in the region was unclear until the signing of the Treaty of Corbeil in 1258 which liberated Catalonia and Languedoc. It also fixed the border as just south of Peyrepertuse Castle. Like its neighbors, the castles of Puilaurens and Queribus, Peyrepertuse was one of the royal fortresses which was reconstructed at the end of the 13th century to defend the border against the Crown of Aragon and then Spain until the 17th century.

In 1355, the castle was restored to its defensive state and Henri de Transtamare, pretender to the Castillian throne, routed at Navarette, was authorized by the king of France Charles V to take refuge there. In 1542, Jean de Graves, lord of Sérignan, seized the castle in the name of the Reformation, but was captured and executed.

The castle was decommissioned as a border point with the Treaty of the Pyrenees in 1659 having lost its strategic importance. Although the citadel was a lot less valuable after the annexation of Roussillon in 1658, a small garrison commanded by a junior officer was maintained until the French Revolution, during which it was abandoned. Sold as a National Property in 1820, its ruins remain today. The first campaign for the preservation of the monument began in 1950.

Since 1908, the site has been listed as a monument historique by the French Ministry of Culture.[2]