The settlement was described by Julius Caesar during his conquest of Gaul under the name of Vesontio. During the Middle Ages, Besancon was part of the Holy Roman Empire and a bishopric. In 1526 it obtained the right to mint coins. Besancon was under Spanish control all the way to the Treaty of Nijmegen (1679) by which it was awarded to France.

In 2003, Besancon was ranked third in France in quality of life. It is characterized by a remarkable balance between dynamic urban development and nature conservation, and is one of France's greenest cities. In the city center, there is a vast park designed by Delacroix in 1843, home to many tree species and offering nice views to the Citadel.

Designed by Vauban and built between 1674 and 1711 on the hilltop, the Citadel is a masterpiece of military architecture and the town's architectural landmark. It dominates the skyline at daytime, and is beautifully illuminated at night. The Citadel houses the rich ethnographic collection of the Comtois Museum, and the Resistance and Deportation Museum recounting some of the darkest moments of 20th-century history. The city zoo and the natural history museum are also within the Citadel. From the thick ramparts, there is a great view on the old city and its Grand Rue, the main street since Roman times.

Vauban also built a number of fortifications around the city: Fort Chaudanne, Fort de Trois Chatels, Fort Griffon, Fort Beauregard and Fort des Justices. A funicular used to run to Bregille Heights but it was closed down in 1987.

The beautiful old town lies between the curve of the Doubs and the Citadel. Almost untouched by modern architecture, it contains stone buildings dating back to the Middle Ages. The proximity to Switzerland can be felt in the architectural similarities.