The Judicial Branch can declare an Executive Order (a Presidential Order) unconstitutional if it is presented to the court as part of a case or controversy.
While the US Supreme Court is the final arbiter of constitutionality, even US District Courts can overturn an Executive Order, as was the case with President Obama's moratorium on deep water drilling in the Gulf. The lower court's decision may be appealed all the way to the Supreme Court, but in this instance it wasn't.