A file photo of the New York City subway. PHOTO: REUTERS
Abid Naseer, 26, is also accused of participating in other plans for attacks in Norway and Britain.
He entered his not guilty plea in a Brooklyn federal court through his lawyer, Steven Brounstein, the federal prosecutor said.
The judge ordered Naseer to remain in detention until his next hearing on March 7.
The US justice department said in July Naseer had been charged with conspiring to use weapons of mass destruction and to commit murder abroad, supporting al Qaeda, as well as "committing and attempting to commit an act of terrorism transcending national boundaries," among other counts.
Naseer was first arrested in 2009 in northern Britain in a counter-terrorism operation along with 11 other men suspected of preparing an attack against a shopping centre in Manchester.
They were all released without charges, but he was then arrested for a second time in July 2010 at the request of Brooklyn prosecutors, who accused him of participating in the plot to attack the New York City subway in 2009.
In the federal indictment, Naseer is named co-defendant along with Bosnian-born American Adis Medunjanin, who was sentenced in November to life in prison for the plan, in which Medunjanin aimed to turn himself into a suicide bomb in the subway as revenge for American attacks in Afghanistan.
Two other men in the alleged plot, high school friends of Medunjanin, pleaded guilty and testified against him and await sentencing later this year.
Naseer had done scouting for these attacks, but the plan unravelled when Medunjanin realized he was under surveillance and tried to get rid of the evidence.
Federal prosecutor Loretta Lynch called it one of the most serious plots since September 11, 2011, saying at Medunjanin's sentencing that "scores of innocent New Yorkers would have been killed or maimed had Medunjanin succeeded."
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@BruteForce: "Not a single Terrorist attack after 9/11 with a sizeable Muslim population. Remarkable achievement."
Hamid Gul still says that US intelligence failed on 9/11 not realizing that muslims were not viewed with suspicion that much before 9/11, and this retarded is well respected in Pakistan.
"conspiring to use weapons of mass destruction"
Just a lame excuse to book anyone on terrorist charges...
Not a single Terrorist attack after 9/11 with a sizeable Muslim population. Remarkable achievement.
Terrorist tend to plead not guilty when they are charged - but before the trial stage begins the prosecutor is required to share evidence with the defendant which usually resorts in a plea bargain - no doubt this terrorist will follow a similar path.