Francisco Guillermo Flores Perez was born 17 October 1959 in El Salvador's second largest city, Santa Ana. He is the son of a well-known lawyer and an ethnographer. Unlike his party's last two presidents, who were conservative businessmen, Flores was previously a philosophy professor. Flores received his bachelor's degree in political science from Amherst College in Massachusetts and studied philosophy at World University, a small unaccredited institution in Ojai, California. In the early 1980s, he visited India several times to study mysticism and philosophy under Hindu swami, Sri Sathya Sai Baba, who preaches tolerance, patriotism, and nonviolence. Despite this training, Flores considers himself to be a devout Roman Catholic. During the late 1980s, he lectured at the Central America University (UCA) and Jose Matias Delgado University.
Leftist guerrillas were responsible for the death of Flores's grandfather and father-in-law. But Flores did not participate in the civil war. Instead he attended college and graduate school, taught philosophy, and managed an irrigation project for a community of 300 families living adjacent to the cattle ranch and stud farm he had inherited from his grandfather. He joined the government in 1990 in ministerial and advisory positions before becoming elected to the National Assembly in 1994. By 1998, he had become head of his party's congressional delegation and the assembly's speaker. Known by the nickname of "Paco" or "Paquito," Flores is an expert horse tamer. His wife, Lourdes Rodriguez, is a schoolteacher. They have two children, a daughter, Gabriela, and a son, Juan Marcos.