Founded in 1850, Bontoc derived its name from a creek called Bontoc in the pueblo of Lungsodaan, which existed during the occupation of the Spaniards in the country. At that time, the place was still under the municipality of Libagon.
When the Americans took over, Bontoc became a barangay under the municipality of Sogod. It was only on June 15, 1950 that Bontoc became a separate town composed of 40 barangays by virtue of Republic Act No. 522.