Ahmed Khalfan Ghailani, a Tanzanian national, is to face charges over his alleged involvement in the 1998 bombing of two US embassies in Africa.
The al-Qaeda suspect has been held at the notorious prison camp in Cuba since 2006.
He is expected to make his first appearance in a Manhattan federal court later, according to US Attorney General Eric Holder.
'Ahmed Ghailani is being held accountable for his alleged role in the bombing of US embassies in Tanzania and Kenya and the murder of 224 people,' he said in a statement.
Mr Ghailani faces 286 counts of murder, conspiracy to murder, bomb and maim and conspiracy to use weapons of mass destruction against US nationals, charges for which he could receive the death penalty.
According to the indictment from March 2001, Mr Ghailani also conspired with al-Qaeda leader Osama bin Laden and other Qaeda members to kill US citizens.
US President Barack Obama is under intense pressure to decide the fate of the detainees from 30 nations at Guantanamo, many of whom have not been charged.
He has vowed to close Guantanamo by January 2010.
The prison still houses about 240 inmates, most of whom have been detained since the 11 September, 2001 terror attacks on the US.
