The Dominican Fathers worked for the foundation of San Fabian for two reasons: first, to make it, on account of its climate, as a place of infirmary for their order and second, for the conversion of the Igorot pagans then living near the Christian settlements. To effect its founding in 1717, the main settlement in Barangay Anguio was moved to the site of the present church.

Fray Francisco Ferrer is credited as the architect of the original construction of the present church erected after the British invation (1762-1765). Burned in 1856, it was rebuilt under the supervision of Fr. Juan Gutierrez, OP between 1857 and 1860. Together with the convent it was damage by earthquake of March 1892 and again during the Hispano-American war in 1898 and the American liberation in January 1945 when the belfry was destroyed. In 1952, it was renovated for the Diocesan Christ the King celebration in the town. Further improvements were done for the Christ the King celebration in 1977.