After a failed first candidacy to the Congress of the Republic at the age of 25, Flores was elected as a councilwoman of Lima in 1986 and re-elected in 1989, after aspiring to the office of Lieutenant Mayor of Lima. She became Deputy of the Republic in 1990, representing Lima. With the Alberto Fujimori's self-coup and the dissolution of the 1992 Parliament, Flores was elected member of the Democratic Constituent Congress in 1992 and re-elected as a Congresswoman in 1995, becoming a leader of the parliamentary opposition to the Fujimori administration. After the fall of the regime, Flores decided to run for President in 2001, finishing in third place with 24% of the national vote in the first round, behind Alejandro Toledo and Alan García. Flores undertook a second run for the presidency in 2006, again occupying the third place in the voting results after being overtaken by Alan García, who went to a run-off with Ollanta Humala. Flores is the first woman to be a major contender for the presidency in the history of Peru.