Platforms were evacuated and the area cordoned off by heavily armed police late on Monday evening.
No details have been given about the operation in one of Europe's busiest transport hubs. But local media report that police were looking for three suspects.
France is under a state of emergency since the Paris attacks of 2015.
Security had been stepped up across the country for the second round of the presidential election, which happened on Sunday.
Le Parisien newspaper (in French) said the operation focused on a train from Valenciennes, in northern France.
Police were looking for three men described as "dangerous" to French security forces by a foreign country, the newspaper said.
They had been spotted in Bordeaux and Marseille, as well as in Paris. Police had launched operations in each city, but had not managed to capture them, the report added.
Footage posted on social media showed many police vehicles guarding the perimeter of the station.
Paris police said on Twitter (in French): "End of security checks. Gradual return to normal."
France has been on a high state of alert since the November 2015 attacks by so-called Islamic State that killed 130 people.
The Gare du Nord train station in the French capital Paris has reopened after a security alert, officials say.