During its long history, Fort de Joux has gone through successive stages of construction. The first construction was built of wood in the 11th century and a rebuilding was executed in stone in the 12th century by the lords of Joux. While others have improved or at least repaired during the course of its history Fort de Joux' most famous remodeler would be Vauban in 1690. Successfully besieged by Austria in 1814, it was later reinforced with the construction of the forts at Larmont during the 19th century. In 1879, Captain (later General) Joffre, then a military engineering officer, modernised it and transformed it into a fort.
It served as a prison for successive French governments between the 17th and 19th centuries. In this capacity, Fort-de-Joux is best known for serving as the site of imprisonment for Toussaint Louverture, who died there on April 7, 1803, Mirabeau and Heinrich von Kleist.
In addition to being employed as a prison, Fort-de-Joux has played a part in the defense of the region up until World War I.
The fortress currently houses a museum of arms which exhibits more than "six hundred rare weapons" dating from the early 18th to the 20th centuries, including a rare 1717 rifle. The castle also has a well which, at 120 m (393 ft), is one of the deepest in Europe.