FBI Director James Comey informed Congress of the move in a letter on Friday, 11 days before the election.
Mrs Clinton told supporters the move was "unprecedented" and "deeply troubling".
But Republican opponent Donald Trump has praised the bureau's decision.
In his letter to Congress, Mr Comey said the FBI had learned of fresh emails which might be "pertinent" to its previous inquiry into the Democratic candidate's use of a private server when she was secretary of state in the Obama administration.