St. Francis Xavier Parish traces its beginnings to a group of Catholics visited by missionary priests as early as 1851. An original church structure was dedicated on November 4, 1860. Under one of its early pastors, the brick structure currently in use was dedicated on September 12, 1880.

The church has had several renovations through the years—some planned and some unplanned due to floods. The Floods of 1937 and 1997 caused great damage to most of Falmouth, including the structures of the parish church, school building, and rectory. The faith of the people of Pendleton County, despite these challenges has never wavered and the parish remains steadfast in the mission of spreading the Gospel of Jesus Christ and “making disciples of all the nations.”