Francisco Guillermo Flores Pérez (born October 17, 1959) was the president of El Salvador from 1999 until 2004 and a member of the Nationalist Republican Alliance (ARENA). He studied philosophy at Amherst College, and entered politics after the assassination of his father in law, chief of staff to Alfredo Cristiani.

He started his political career in ARENA as a vice-minister of Planning (Planificación). Later he served as a vice-minister of the Presidency, with functions as adviser of the head of the State, and directed the plan of governmental action in accordance with the peace accords of January of 1992, that ended the fight with the guerrilla group Farabundo Martí National Liberation Front (FMLN).

In the elections of March 20, 1994, Flores was chosen deputy of the Legislative Assembly and the new president, Armando Calderón Sol, made him secretary of Information of the Presidency.

On March 29, 1998, ARENA announced Flores as their candidate to the presidential elections of the following year. At the age of 39 (the youngest chief executive of the continent), Flores became the 3rd consecutive president from ARENA on July 1, 1999. He served a 5-year term and did not run for re-election. Another member of his party, Antonio Saca, became the next President.

One of the moust outstanding actions taken during his administration was the dollarization of Salvadoran economy. Critics accuse him of doing so without popular consensus, except exclusively with bankers. Even though the replacement of salvadoran colones with dollars proved to reduce interest rates, it also caused inflation due to the upward rounding of prices.

He also had to deal with reconstruction efforts after two powerful earthquakes struck the country in 2001. Delivery of international aid was very inefficient and was therefore denounced by reporters, specifically Marucio Funes from local TV12, which is an affiliate of Mexican company TV Azteca. Instead of taking actions to bring aid more quickly to those in need, further investigations from local journalists showed that Francisco Flores called Mexican president Vicente Fox to ask TV Azteca to shut down reporters of its affliate in El Salvador, in a clear attack to freedom of speech. Later, he also denied TV12 an interview to discuss the issue.

He was also one of the candidates in the running for the office of Secretary General of the Organization of American States, but withdrew on April 8.