The 26-year-old is accused of opening fire at the airport’s Terminal 2, killing five people and injuring six others.
Esteban Santiago is charged with carrying out an act of violence at an international airport resulting in death, which carries a maximum punishment of execution.
He also faces lesser weapons charges.
Esteban Santiago, who is in custody, told agents he had planned the attack and bought a one-way ticket to Fort Lauderdale, according to court papers.
Authorities said they did not know why he chose this target and that terrorism had not been ruled out.
US Attorney Wifredo Ferrer said: “Today’s charges represent the gravity of the situation and reflect the commitment of federal, state and local law enforcement personnel to continually protect the community and prosecute those who target our residents and visitors.”
Esteban Santiago is said to have used a semi-automatic handgun that he apparently legally checked on a flight from Alaska.
Officials were also looking whether mental health problems played a role after it emerged that the suspect had been referred for a health assessment by the FBI.
Two months ago, Esteban Santiago walked into an FBI office in Alaska in an agitated and incoherent state, the FBI and Anchorage police said.
The man was carrying a loaded magazine but had left his handgun in his car, with his newborn child.
During the later mental health evaluation, Esteban Santiago told the FBI he was hearing voices and believed he was being controlled by a US intelligence agency.
His gun was confiscated but the authorities found no wrongdoing, and it was returned in December. It is not clear if this is the same gun that he is accused of using in the attack at the airport baggage claim area.
The suspect is a former member of the Puerto Rico and Alaska National Guard, according to the Pentagon.
Esteban Santiago served in Iraq from April 2010 to February 2011, and ended his service in August 2016.
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