The line to the frontier station at Les Verrières belonged to the Franco-Swiss Company (Compagnie Franco-Suisse, FS) and the section from Les Verrières to Pontarlier belonged to the French Chemins de fer de Paris à Lyon et à la Méditerranée (PLM).

The railway played an important role in the Franco-Prussian War, when during January and February 1871, the French Armée de l'Est with 87,000 men under General Bourbaki retreated into Switzerland and were disarmed and interned in Les Verrières.

On 22 March when the interned troops were released and were being repatriated by train a collision occurred due to an incorrect setting of points at Colombier.

Steam locomotives of the Société nationale des chemins de fer français (SNCF) took over the operation of trains in Les Verrières for the time being.

In 2018, Regio services, operated in collaboration with Transports Régionaux Neuchâtelois (TRN), ran every 30 minutes on the Neuchâtel–Travers section, continuing over the Régional du Val-de-Travers line to Fleurier and Buttes.

As a result, the four-system Thalys high-speed sets and a variant of the Prima electric locomotive were tested on it under 16.7 Hz power when new.