US military prosecutors have filed new charges against Khalid, the self-described mastermind of the 11 September 2001 attacks.
Khalid Sheikh Mohammed, and four alleged co-conspirators are being held at the Guantanamo detention camp.
All five defendants had previously been charged in the war crimes tribunals at the Guantanamo Bay US naval base in Cuba with plotting the hijacked plane attacks that killed nearly 3,000 people in the US.
The charges, which carried the death penalty, were dropped while the Obama administration tried to move the trials into the federal civilian courts.
President Barack Obama yielded to political pressure in April and announced that the prosecutions would be moved back to Guantanamo.
A letter sent to families of 11 September attack victims said fresh charges against Sheikh Mohammed, Walid bin Attash, Ramzi Binalshibh, Ali Abd al-Aziz Ali, and Mustapha Ahmed al-Hawsawi would be filed at Guantanamo today.
Referred to in counter-terrorism circles as "KSM," Sheikh Mohammed is the self-proclaimed architect of the 11 September attacks and a host of other anti-Western plots.
He was subjected to simulated drowning, known as waterboarding, 183 times during his years in US custody and his trial will raise questions about evidence obtained from harsh interrogation methods.
Sheikh Mohammed was arrested in 2003 in Rawalpindi, Pakistan and handed over almost immediately to American agents who held him in secret prisons for over three years before sending him to Guantanamo in September 2006.
In addition to felling the twin towers, he claims to have personally beheaded US journalist Daniel Pearl in 2002 with his 'blessed right hand' and to have helped in the 1993 World Trade Center bombing that killed six people.
Abd al-Aziz Ali, a Pakistani raised in Kuwait who is Sheikh Mohammed's nephew, is believed to have transferred funds to US-based operatives and helped hijackers travel from Pakistan to the United States.
US Republican politicians' gripes at Obama for his U-turn on a military tribunal will intensify now that essentially the same charges are being filed more than three years later.
The Obama administration argues that it has reformed the military tribunals to give greater protections to defendants and ensure that statements obtained by brutal interrogation will no longer be admitted.
In announcing the U-turn in April, Attorney General Eric Holder also has said he still felt a civilian courtroom was the best forum and regretted that a military tribunal was now the only way to go because of blanket Republican opposition in Congress.