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.

Mourinho, 52, is halfway through a four-year deal signed on his return to Stamford Bridge in June 2013.
And further talks are expected in the coming weeks with the club and the Portuguese keen on a long-term option.
In his first spell at the club between 2004 and 2007, Mourinho won consecutive Premier League titles and succeeded this season with three games to spare.
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The 2005 title was Chelsea's first top-flight success in 50 years and he also delivered two League Cups and an FA Cup.
But he left the club to eventually join Inter Milan after falling out with Chelsea owner Roman Abramovich.
Since his return after a six-and-a-half-year absence, which included three seasons at Real Madrid, Mourinho has spoken of his desire to stay as long as the Russian billionaire wishes to keep him.
The Blues boss repeated that after Sunday's 1-0 defeat of Crystal Palace, which secured Chelsea's first title since 2010 and the eighth of his prolific career.
"As I was saying since the beginning of the season, I stay here until Mr Abramovich wants me to stay. The day he tells me to go, I go," said Mourinho.
Mourinho is still to win the Champions League with Chelsea, a competition he has won with Porto and Inter Milan.

Cynthia Cheroitich, 19, said she drank body lotion because she was hungry and thirsty.
She was only brought out on Saturday morning after security forces found a teacher she knew to convince her it was safe to come out.
Ms Cheroitich said her ordeal began at around 05:30 (02:30 GMT) on Thursday when she and her fellow students were in class studying for their exams.
"Suddenly, we heard the bullets and then we started coming out and then we said: 'What is happening?'" she told the Associated Press news agency.
"We ran to our rooms, then these people came running, following us. When we reached our rooms, we hide under the beds."
She said that their pursuers told them to come out of their hiding places, but she decided to hide in the wardrobe instead where she covered herself with some clothes.
It was then that the gunmen entered the room. Ms Cheroitich described a scenario that other survivors have alluded to.
Her roommates were taken out and divided up between those who were able to recite verses of the Koran and those who were not.
It was not clear what happened to them.
She said she found some bottles of body lotion where she was hiding and "drank all of them", describing it as "nice and lovely".
But she was too scared to move. "I was just praying to my God," she said.
It was not until 10:00 on Saturday, long after the attack ended, that the authorities were able to persuade her to come out.
She told AP: "You know at first I did not believe it [when police came to rescue her], at first I was thinking that maybe they were the al-Shabab.  So I said: 'How do I know that you are the Kenyan police?'"
It was only after a member of the college staff came to convince her that it was safe to come out that she emerged.
The Gare du Nord train station in the French capital Paris has reopened after a security alert, officials say.
[NEXT_CONCEPT]
Chelsea boss Jose Mourinho is close to agreeing a new contract after securing a third Premier League title.
[NEXT_CONCEPT]
A survivor of the al-Shabab attack on Kenya's Garissa university campus has been describing how she spent more than two days in a wardrobe in fear of rampaging militants.