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.
On the May 1st, Brazil joined these two countries in a secret alliance (the Treaty of the Triple Alliance), which stipulated that they should unitedly prosecute the war until the existing government of Paraguay should be overthrown "until no arms or elements of war should be left to it." This agreement was literally carried out.
Flores' victory came at the expense of the Farabundo Martà Front for National Liberation (FMLN), the political party formed from the guerrilla front that fought the Salvadoran army to a stalemate over 12 years of civil war, from 1980 to 1992.
Flores will also be challenged on key aspects of the 1992 peace accords that have failed to meet expectations, especially regarding human rights, the new civilian police force and reform of the judicial system.
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