Abid Naseer was extradited from Britain late last week. He entered the plea in federal court in Brooklyn through his attorney, Steven Brounstein. The lawyer declined to comment outside court.
The judge ordered Naseer held without bail until his next court date, on March 7.
Prosecutors aim to prove that Naseer collected bomb ingredients, conducted reconnaissance and was in frequent contact with other al-Qaida operatives. If convicted, Naseer, 26, could face up to life in prison.
Naseer was one of 12 people arrested in a counterterrorism operation in Britain in April 2009, but all were subsequently released without charges. They were ordered to leave the country, but Naseer avoided being deported to Pakistan after a judge ruled it was likely he would be mistreated if he were sent home.
Authorities rearrested Naseer in July 2010 at the request of prosecutors in Brooklyn, where a federal indictment named him as a co-defendant with Adis Medunjanin, a U.S. citizen from Bosnia. The prosecutors also alleged he was part of a broader terror campaign that would have targeted Britain and Norway.
Lawyers for Nasser fought his extradition, arguing that the American government would have fewer inhibitions about returning him to Pakistan. But in January 2011,
U.S. authorities allege Medunjanin and two friends from Flushing High School in Queens—Najibullah Zazi and Zarein Ahmedzay—traveled to Pakistan in 2008 to seek terror training from al-Qaida.
Zazi, an airport van driver from Colorado, admitted in a guilty plea that once back from Pakistan he tested peroxide-based explosive materials in a makeshift lab in Denver in the fall of 2009 before traveling by car to New York to carry out the scheme. The men abandoned the plot after they learned they were being watched by investigators.
Zazi and Ahmedzay, who also pleaded guilty, are awaiting sentencing.
Medunjanin was sentenced to life in prison after a guilty verdict at a trial last year. At his sentencing, he recited verses from the Quran and said he had "nothing to do with any subway plot or bombing plot whatsoever."