Halligan, who is currently the general counsel for the Manhattan district attorney’s office, was nominated by President Barack Obama.
Obama still has not secured Senate approval for a single nomination to the D.C. Circuit. The court has four vacancies on its 11-member panel.
In a statement, Obama said he was “deeply disappointed” in the vote.
Halligan could not immediately be reached for comment.
The Senate voted 51-41 to end debate on Wednesday and proceed to a floor vote on the nomination, short of the 60-vote supermajority required to overcome a filibuster. Alaska Senator Lisa Murkowski was the lone Republican to support Halligan.