San Manuel started as a mission under the parish of Aurora (which was canonically erected in 1951). The different ministries were performed by the then assigned priests starting from Fr. Paul Douillard, MS+ followed by Fr. Lionell Lacasse in 1954 and the other priests like Fr. Frank Bourgeouis, MS and the rest of the La Salette Missionaries who followed after from 1951 to 1986.

It started functioning as a sub-parish in 1990 with Fr. Job Callarackal, MS as the priest in-charge. It was also during the term of Fr. Callarackal that a kindergarten was established in San Manuel to cater to the initial Catholic educational formation of the children of the Catholic families in the locality.

On February 11, 1996 the sub-parish was canonically erected as a parish, with Fr. Francisco Tamani, MS as the parish priest. Fr. Tamani, MS stayed in the parish for only a year.

On May 15, 1997, FR. Jacob Vettathu, MS took over as a parish priest. He started the various programs of the parish such as the PREX (Parish Renewal Experience), PRAYER (Parish Renewal Encounter for Youth) and the formation of the BEC (Basic Ecclessial Communities) in the different barangays.

On Easter Sunday, April 11, 2004, administration was officially turned over to the Diocese of Ilagan during a Eucharistic celebration celebrated by Bishop Sergio Utleg, DD