In 2000, Congressman Antonio M. Diaz ordered the construction of building intended for a high school in the barangay beside the San Rafael Elementary School. Through the funding of the national government via the Department of Education, the school structure was completed in 2001.

            Nevertheless, despite the completion of the building, it just remains a building until 2005. For some unknown reason, it was not utilized, which causes some of the facilities to be stolen and some others to be destroyed.

            In 2005, the buildings were used as an extension of the Maloma National High School, with 57 students who are enrolled in MNHS but are residents of Brgy. Sto. Niño, San Rafael, Manglicmot; barangay which are adjacent to the school premises. One of the problems encountered, however, was the inability of the teachers from MNHS to attend to their classes on time because they still had classes in the main campus which incidentally is 5 km. away from the school.

            Through the motion of SB Member Usaffe Basa, SB- In charge of Education, a resolution requesting the opening of San Rafael High School as a complete high school was passed. Perlita C. Basa, Ph. D. CESO V, Schools Division Superintendent supported this move and later on inaugurated the school on July 05, 2006.

            It was managed by the elementary principal; who was believed has the capability and hard works of being a leader of both school, Nellie F. Frondarina. In spite of the many task on her shoulders made a legendary mark when San Rafael, on its first operation as a complete high school was regarded as one of the top performing high schools based on the 2008 National Achievement Test (NAT).