The first settlers in Tubigon settled along the shores of the river that flows through the community. Their exact origins are unknown but they are thought to be early Malays from southeast Asian countries, migrating to the Philippines in small bangkas. Seasonal overflowing of the river flooded the community and led the place to be called “Tubigan” (meaning “place having water” or “watery”), which later morphed into “Tubigon” (meaning “place abounding in water”). The first record of the town of Tubigon dates from the early part of the 17th century.

In 1816, the community organized itself under a recognized headman, Yguiz Hutora, who was succeeded by teniente Mijares and by teniente Matong in 1818. A chapel was built on an elevated site of the settlement but had no officiating priest. A coadjutor of the Spanish friars from the Calape parish would perform the religious ceremonies.

In 1819, by authority of the Spanish Governor of Cebu, Tubigon was formally organized into an independent town by separating from the town of Calape, with Capitan Teniente Matong becoming the first gobernadorcillo.

Starting in 1852, the exact boundaries of the municipality were defined. On 8 March of that year, sitio Bacane was made the boundary between Tubigon and Inabanga. In 1856, the boundary with Calape was fixed at Mandaug. On 19 June 1865, the boundary between Tubigon and Catigbian was set at the Sampilangon River and on 14 September 1913, the boundary with Antequera (currently San Isidro) was fixed at sitio Tubod.

On 31 January 1919, Tubigon lost five barrios when Clarin was formed by virtue of proclamation by Governor Yeater.

Tubigon was badly affected by the 2013 Bohol earthquake, suffering 11 fatalities and damage to some 7,300 homes, as well as total destruction of its town hall and church.