The man was arrested after two hours when a swat team backed by a dog moved into the station, Dutch police said.
Half of the platforms and much of the central station had to be cleared during the operation to arrest the man, whose motives remained unclear.
"Thanks to the arrest team and the dog, the man has been taken out of the toilets and was arrested in the Thalys," Dutch police said in a message sent on Twitter.
The incident came less than a month after a suspected jihadist opened fire on a Thalys train from Amsterdam to Paris, injured two people.
The gunman armed with a Kalashnikov had opened fire on the high-speed train on August 21, carrying more than 550 passengers -- but, almost before bystanders had time to react, he had been overpowered by several passengers including off-duty American servicemen.
The Thalys train company, which mainly operates services from Paris to Amsterdam via Brussels, said Friday there was "no danger for our passengers." But all train services to Rotterdam remained suspended.
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