The alleged mastermind of the 9/11 destruction in New York, Khalid Sheikh Mohammed, will be tried by a military commission at Guantanamo Bay.
Four other men will also be tried at the infamous military camp.
The Obama administration had wanted the men to be tried in a civil court but later backed down when opposition arose.
While President Obama had in 2009 pledged to close Guantanamo Bay, he more recently lifted a two-year freeze on any new military trials at Guantanamo Bay in Cuba.
White House spokesman Jay Carney said on Monday: “The President’s primary concern here is that the accused perpetrators of that terrible attack on the American people be brought to justice as swiftly as possible, and as fairly as possible.”
Much of the opposition to trying inmates in US courts was that Guantanamo Bay prisoners should not have full US legal rights.