The fort was initially nothing but a bastion built as a component of the wall around the Croix-Rousse hill at the beginning of 16th century by François I, to protect the town from the Swiss.

The fort was completed in the 18th century, but construction of the current building began in 1834.

In 1984 the fort was occupied by the Veterinary Service of the Armed Forces.

Rehabilitated in 2001 by architect Pierre Vurpas, Fort St. Saint-Jean has been home, since 2004, to the National Treasury School (ENT) which became the National School of Public Finance (ENFiP) on 4 August 2010.

This school trains public finance controllers and occasionally hosts cultural events.