[2] The RER line C section of the station dates back to 1900, when it opened as the Pont Saint-Michel station on the extension of the Compagnie du chemin de fer de Paris à Orléans from the Gare d'Austerlitz to a new terminus at the Gare d'Orsay.

The Pont Saint-Michel station was built under the quays of the Seine, almost at river level, and its constrained location, with narrow and low platforms and reverse curves, affects operations to this day.

Originally the platforms were lit by openings in the river bank, but these were filled in after the station was inundated during the Seine floods of 1910.

[citation needed] On 25 July 1995, as part of a campaign of terror bombings conducted by the Armed Islamic Group of Algeria, the station was the target of an attack, with a gas bottle exploding near one of the line B platforms, killing eight and wounding 80 people.

The principal improvement was the reinstatement of natural lighting by replacing the original openings, closed in 1910, with 28 large windows that are designed to withstand flooding.