The company, operated jointly by SNCF, the French rail company, and Swiss Federal Railways (SBB), said it would be replaced by TGV service on a direct route via Basel.
Last December, Lyria served warning that it was considering scrapping the route, which also has stops in the French towns of Pontarlier, Frasne, and Dijon, because it was losing too much money.
At the time, Lyria general manager Alain Barbey said the TGV route through Neuchâtel was running a deficit of 2.3 million francs ($2.4 million) a year.
The company said the new direct route through Basel would reduce the length of the trip by 15 minutes.
In a press release, Lyria noted that many passengers were already travelling between the French and Swiss capitals by making a transfer at Basel.
“Since the opening of the Rhine-Rhone high-speed line in December 2011, customers departing from Bern wishing to go to Paris have favoured an itinerary with a transfer at Basel,” the company said.
Officials in Neuchâtel and neighbouring communities in France were disappointed by the decision.
More than 20,000 people had signed a petition to maintain the TGV route.
SBB and SNCF are promising to provide alternative, high-quality service to serve towns on the Neuchâtel-Paris route.