U.S. District Judge Raymond Dearie ordered Abid Naseer, 26, held without bail after his appearance in federal court, Voice of America reported.
Naseer's court-appointed attorney, Steven Brounstein, entered the not guilty plea on behalf of his client and declined to answer questions from the press.
Naseer was indicted in November 2010 in Brooklyn on a charge of providing material support for al-Qaida. The indictment was part of a larger case involving three men who were convicted of plotting to blow up New York subways during rush hour.
Britain extradited Naseer last week. His next court date was set for March 7.