The man was arrested after flying in from Liverpool, England, and before he flew out to Uganda, prosecutors' spokesman Evert Boerstra said, without specifying what terror group was involved. His name and age have not been released.
"He was arrested on the tip-off from British authorities," Boerstra told The Associated Press.
Dutch state broadcaster NOS reported that the suspect is allegedly linked to Somalia's most dangerous militant group, al-Shabab, which has claimed responsibility for suicide bombing attacks at U.N. facilities and other targets, including July attacks in Uganda's capital during the World Cup final that killed 76 people.
Al-Shabab said those blasts were in retaliation for civilian deaths caused by African Union troops in the Somali capital, Mogadishu, and the group has called for Uganda to withdraw its peacekeeping forces from Somalia.
Militant veterans of the Iraq and Afghanistan conflicts help train al-Shabab fighters, one of the reasons the sophistication of its attacks has risen in recent months. The al-Qaida-linked group in the past has recruited Somali-Americans to carry out suicide bombings in Mogadishu.
The chief of Britain's domestic spy agency MI5, Jonathan Evans, said Thursday that would-be terrorists from around the world, including dozens of people either born or living in Britain, were training in al-Shabab camps.
Dutch prosecutors could not immediately confirm the NOS report.
London's Scotland Yard said it would make no comment, while authorities at Liverpool's John Lennon Airport said they had no knowledge of the arrest. A spokeswoman for Liverpool's police force said she had no information on the arrest, while Britain's Foreign Office said it was looking into the matter.
Schiphol is one of Europe's largest airports, and a major transit point for flights to the Middle East and Africa.
Amsterdam's airport has significantly beefed up its security measures since last December, after it was a departure point for a Nigerian student, Umar Farouk Abdulmutallab, who allegedly tried to blow up a plane above the United States on Christmas Day by setting off explosives hidden in his underwear.
He was tackled by passengers and crew, and is now charged in U.S. federal court in Detroit with attempting to blow up Northwest Airlines Flight 253 with 278 passengers and 11 crew members aboard. Abdulmutallab is representing himself, but a judge has appointed a standby lawyer to assist him.
After the Abdulmutallab lapse, Schiphol ordered 60 new full body scanners to screen passengers flying to the United States.
Last month, two Yemeni men were arrested at the Amsterdam airport after flying in from Chicago, on suspicion they may have been conducting a dry run for an airline terror attack. The two were held for several days then released without charge after an investigation turned up no evidence to link them to a terror plot.
Associated Press Writer Raphael G. Satter in London contributed to this report.