It is believed that the very first Catholic Mission Chapel was built sometime in the sixteenth century on a lot across the present Church. As history tells, the island of Rota was serviced by a priest from the Diocese of Cebu, Philippines. Records of Sacraments celebrated were taken by whoever was sent to be recorded at Cebu.

The first Baptismal record in the San Francisco de Borja Parish shows Albert Vincent Duenas, baptized on April 21, 1912, by Father Corbinian, O.F.M. Cap.

The present Church was started after World War II and was finished in the early 1950s.