Balaguer studied law at the Sorbonne, then returned to the Dominican Republic and started working for Trujillo in 1930. After Trujillo was assassinated in 1961, he fled to the United States. In 1963, a military coup overthrew the leftist government of Juan Bosch. In 1965 military officers revolted against the junta to restore Bosch, whereupon U.S. President Lyndon Johnson sent 20,000 U.S. troops to defeat the revolt. Balaguer became the President of the Dominican Republic in 1966, with U.S. backing. He governed the country until 1978, when he was defeated at elections by Antonio Guzmán Fernández, leader of the Partido Revolucionario Dominicano political party.
He returned to office in 1986. This second government was in some aspects different from the first one (commonly referred as "The Twelve Years").
He left office for the second time, reluctantly, in 1996, but was a power in Dominican politics to the very end of his life. He died of heart failure in 2002. Balaguer never married and had no children; he was survived by a sister.