Faruq Khalil Muhammad 'Isa entered the plea on Saturday in federal court in Brooklyn.
Muhammad 'Isa was arrested in Edmonton on a U.S. warrant in 2011.
An indictment accused him of helping co-ordinate Tunisian jihadists believed responsible for a suicide attacks that killed five American soldiers outside a U.S. base in Iraq in 2009.
The 36-year-old Muhammad 'Isa was taken to New York City on Friday.
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