The city historically was an important transportation hub. The first rail line in Canada connected it with La Prairie in 1836. The Chambly canal extends 20 km north along the west bank of the river and provides modern freight passage to Chambly and the St. Lawrence River.
Known to the early English settlers as St. Johns, the site was fortified in the 17th century. Later the French built Fort St. Jean on the site. It provided an important communication link during the French and Indian Wars. During the American Revolutionary War control of the town changed hands several times as the British and American forces moved through the area.
Today's St. Jean has textile, food and wood products manufacturing. It hosts the Collège Militaire Royal de Saint Jean, a bilingual military academy. In 2001, a new city organization was created as a regional county municipality including several adjoining communities, and population was adjusted to 39,720.