At issue is an anti-terrorism law that Bush pushed through Congress last year taking away the right of the foreign terrorist suspects held at the U.S. prison at Guantanamo Bay in Cuba to have a judicial review of their detention.
The decision by the court to hear the two cases was a setback for the Bush administration which had urged the justices to turn down the appeals.
There are about 375 detainees now at the prison which critics, including some of Washington's allies, have demanded be closed. The first arrived more than five years ago after the United States launched its war on terrorism in response to the Sept. 11 attacks.
The indefinite detention and allegations of prisoner mistreatment at Guantanamo, which the U.S. military denies, have tarnished the U.S. image abroad. Human rights groups have demanded Guantanamo be closed and detainees charged with crimes or released.
Three of the nine justices in April dissented from the decision to reject the appeals by the Guantanamo prisoners. The high court on Friday gave no explanation for its reversal in now deciding to hear the cases.
After the appeals had been rejected in April, lawyers for the prisoners asked the court to reconsider, and the court on Friday agreed. It has been the first time in decades the high court has granted such a request.
The Supreme Court's action in the Guantanamo cases was announced the day after the justices had ended their 2006-2007 term.