Originally occupied in the 4th century B.C. by the Sequani, a Celtic tribe, the region became a part of the Roman Empire after Julius Caesar's victory over the Gauls in 52 B.C. It was later settled by the Burgundians and, in 534 A.D., conquered by the Franks.
In the 10th century the various small countships of the area were united to form the county of Burgundy, a fief of the kingdom of Burgundy. The county passed, with the kingdom, under the suzerainty of the Holy Roman Empire in 1032. The name Franche-Comté ("Free County") first appeared in an official document in 1366.
In 1384, Franche-Comté passed through marriage to Philip the Bold, duke of Burgundy, under whom it received a definite political organization — council, estates, parliament — centered in Dôle. As a result of dynastic marriages, it was severed from Burgundy and ceded to the Habsburgs in 1493 by the Treaty of Senlis. After the reign of Emperor Charles V, it passed in 1556 to the Spanish branch of the Habsburgs.
Under Spanish rule the province fared well and was granted a large measure of autonomy. The parliament of Dôle was the political center, and the governor was chosen from the ranks of the Franche-Comté nobility. Moreover, the obligatory money payment to Spain was small, and few of the province's inhabitants were taken as soldiers. Franche-Comté's prosperity was symbolized by Besançon's fairs and the many new Renaissance structures built.
Franche-Comté was often invaded by the French and was devastated during the Thirty Years' War. Spain forcefully defended the region, no doubt because of its military importance; it not only connected the Spanish possessions in Italy and the Low Countries but also allowed for the opening of another front against France in case of war. In 1665, however, Louis XIV laid claim to Franche-Comté in the name of his wife, Maria Theresa, and three years later the prince de Condé conquered it in 15 days. Louis swore to maintain the province's liberties but was forced to return it to Spain by the Treaty of Aix-la-Chapelle. Another successful invasion was staged shortly afterward; both the king and the fortification expert Vauban were present at the lengthy siege of Besançon in 1674. The arch of Saint Martin's Gate in Paris was erected to celebrate Franche-Comté's definitive annexation in 1678 by the Treaty of Nijmegen.
Although Besançon, the new capital of the province, was given a parliament and a university, anti-French sentiment remained strong until the 18th century, when Frenchmen from surrounding districts began to settle there. In 1790, as part of the administrative reforms brought about by the Revolution, the old province was divided into departments. Franche-Comté was resurrected as an administrative region in 1982.