Francisco Pérez first competed in the Vuelta del Uruguay cycling race in 1957 and finished 21st, while the following year he was 22nd. In 1959, however, he was the runner-up in that competition, having come in first in Stage 8. From then on, he was a regular on the podium at national races and was eventually selected to represent Uruguay at the 1964 Tokyo Olympics. There, he was 48th in the road race and 10th in the 100 kilometers team time trial, alongside Wilde Baridón, Vid Cencic, and Ricardo Vázquez. He also competed at the UCI Road World Championships in 1964 and 1966, placing 56th in the road race at the former tournament and 16th in the 100 kilometers team time trial at the latter, with Óscar Almada and the non-Olympians Orlando Aguirre and Franklin Placeres. Pérez retired from active competition in 1970.