Akayed Ullah entered the plea today after he was indicted a day earlier on charges he provided material support to a terrorist organisation and used a weapon of mass destruction.
Ullah was the only person seriously hurt on December 11 when the bomb went off in a corridor linking the subway to Manhattan's Port Authority bus terminal.
Authorities said Ullah taunted President Donald Trump on Facebook before the attack. The president later demanded tightened immigration rules.