Francisco Funes took up cycling after his uncle gave him his first bicycle, with him soon joining a newly formed cycling team in his native El Salvador. Funes began to train very hard, getting up at 3 AM each morning to cycle 100 kilometres or more from Santa Tecla to Comalapa and back. The training paid off with him being selected to represent his nation at the 1968 Mexico City Olympics, riding in both the road race and the team time trial. Funes continued to compete in races throughout Central America, with his biggest victory coming in 1973, winning the overall classification at the Vuelta a El Salvador.
El Salvador