Flores, 56, had been in coma since undergoing emergency surgery.
Flores, who led El Salvador from 1999 to 2004, was under house arrest on charges of embezzlement and illegal enrichment. He was accused of diverting more than $15 million, which had been donated by Taiwan to help the victims of earthquakes in 2001. A court said that $10 million of that went to the party that carried Flores to power and the remainder to him.
Doctors last week had said that Flores had suffered irreversible neurological damage and that his chances of survival were minimal.
Flores had suffered from thrombosis, the clotting of blood in veins. He was hospitalized for that in October 2014, and again Dec. 22, 2015, for an internal hemorrhage.
Loyda Robles, one of the plaintiff lawyers against Flores, said last week that his death would end the criminal prosecution, but that the civil litigation would continue.