Originally named as Kaniug (from liug, or neck) of a river when the early settlement was established between two rivers. The community was made into a town by the Philippine Government in 1899, with Miguel Tio as chieftain. It was officially made a municipality in 1951 by Executive Order No. 192 issued by President Elpidio Quirino.
Migrants from Bohol, mostly Catholics and all inhabitants agreed to change the name of the town after a saint: San Fransisco. An image of San Fransisco was ordered but did not arrive. Instead an image of San Isidro was missent to the residents of San Fransisco. Thus while the name is San Fransisco, the patron saint is San Isidro.