Major Nidal Hasan, 42, faces the death penalty if convicted.
Hasan has repeatedly attempted to plead guilty but the request was denied because prosecutors were unwilling to waive the death penalty, and military law does not permit people to plead guilty to a capital offense.
However, military judge Colonel Tara Osborn agreed to let Hasan represent himself at trial after a military doctor testified that he was fit to handle the physical strain.
"The judge further ruled that defense counsel Lieutenant Colonel Kris Poppe and Major Joseph Marcee may continue to act as stand-by counsel and will sit with Hasan throughout the trial," Fort Hood said in a statement.
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The massacre jolted the US military and prompted calls for stronger safeguards against possible internal security threats and "homegrown" terror attacks.
The FBI alleges Hasan had contacts with firebrand US-born cleric Anwar al-Awlaqi, a key leader of Al-Qaeda in the Arabian Peninsula who was killed in a 2011 drone strike.
Hasan, who was born in Virginia to Palestinian parents and raised in the eastern US state, had attended a mosque in 2001 where Awlaqi worked and is believed to have continued to communicate with the radical cleric.
The Pentagon has refused to call the shooting rampage at Fort Hood a terrorist attack, classifying it instead as an act of workplace violence.
Hasan was set to deploy to Afghanistan weeks after the attack.