The suspect, identified only as Sabir K. under Dutch privacy laws, was arrested in Pakistan last year and expelled to the Netherlands where he was sent to a high-security jail pending extradition.
In a written ruling, the Netherlands' highest court rejected K.'s argument that he should not be extradited because he was tortured in Pakistan and that Americans were involved in the abuse.
He was indicted last June by a federal grand jury in New York.
The Supreme Court said its ruling cleared the last legal hurdle to K.'s extradition, which must be approved by the Dutch government, but his lawyer vowed to fight on.
"It is disappointing, but we still hold out hope this man will not be extradited," attorney Andre Seebregts told The Associated Press in a telephone interview.
"We will now go to the minister for security and justice and should he agree with the extradition we will file and injunction in The Hague and after that we could go to the European Court of Justice," Seebregts added. "We are not done."
Seebregts said he had not spoken to his client to get his reaction since the ruling was issued.
In an unusual move, the Dutch Foreign Ministry released a statement last year saying that the Dutch consul in Pakistan visited K. twice while he was in detention and saw no signs of abuse, though it noted he was blindfolded coming and going to the visits.
The foreign ministry rejected claims by K. that the Dutch government assisted U.S. authorities by luring him to the Netherlands with false promises he would be freed once he left Pakistani soil.
According to a Dutch summary of the U.S. indictment, K. worked for and with al-Qaida between 2004 and 2010. It says he tried to kill U.S. soldiers in Afghanistan, including planning a suicide attack on a U.S. military base in Kunar province in 2010.
He was also charged with possession and use of guns and "destructive material," presumably explosives, during attacks on U.S. troops.