San Juan Elementary School was established and opened as primary school in 1957 by the late Mr. Pedro Tumaneng as the lone teacher handling Grades 1 to 3. It was in 1995 that the school started to operate as a complete elementary with three teachers handling combination classes and culminated its first closing program on March 1996.

The school's achievements and accomplishments were attained through the leadership of competent school heads from Mr. Pedro Tumaneng to Mr. Villamor D. Taberna to Mrs. Aning dela Cruz to Mr. Gines Maggay to Mr. Angel T. Diesto Jr to Mrs. Consolacion Resurrecion to Mrs. Nieves Quinan to Mr. Carlito A. Taberna to Mrs. Ma. Teresa S. Lazatin and back to Mr. Carlito A. Taberna as the first Head Teacher III to manage the school in 2006.

At present, the school offers complete elementary including Kindergarten with one hundred fifty -five (155) learners. The school has a plain topography with a total land area of 7.450 square meters. It has four (4) buildings with 7 instructional and (2)non-instructional classrooms. Seven rooms are used for instructions and two serve as non-instructional rooms ( school Office, and Computer room). The school is now under the supervision of Mrs. Rowena D. Balubal, Head Teacher III with seven(7) competent and capable teachers.

While the school is dependent on external support and on the DepEd Central Office (CO) down to the Schools Division Office (SDO) in many aspects of delivering basic education services, it also operates functionally by utilizing its available resources and by judicious spending of its Monthly Operating and Other Expenses (MOOE) downloaded from the CO. The school MOOE has increased to nineteen thousand three hundred pesos (PhP19,300.00). School canteen funds also help in the operation of the school for various local competitions , photocopying of reports and many more.

The school has organized a functional PTA that supports the different projects and activities of the school. Working hand in hand with the PTA is the Child Protection Committee that ensures protection of the school children.

Driven by the Department of Education's vision and mission to continuously improve itself to better serve its stakeholders particularly its learners, the school has been doing its share in implementing programs of the Department.