St. Francis High School, formerly named St. Joseph's Academy (Boys' Department), came into existence in 1950. This educational institution was established in response to the pressing need for religious formation of the youth in the community. With the administrative assistance of the Franciscan Missionaries of Mary, headed by Mother Maria Mildreda, Rev. Fr. Brigido D. Nantes formally opened the school with the purpose of developing young men into individuals who are morally, physically, intellectually, emotionally, and socially fit.

After his death, Rev. Fr. Brigido D. Nantes’ aspirations to develop the youth according to the life and teachings of St. Francis were continued by the tandem of Mr. Fernando Nantes and Mrs. Charito Nantes, who assumed the leadership of the school in 1982. In keeping with its growing mission, the school began accepting female students in School Year 1991–1992.

With the vision of expanding the Assisian community, the school transferred to a brand new campus in Munting Bayan. Bigger and better facilities were prepared for School Year 2005–2006 to continue serving the educational needs of the modern youth.

Firm in its belief in providing quality education to the youth of Sariaya, St. Francis High School began offering Kinder 1 and Kinder 2 in School Year 2014–2015, followed by Grades 1 to 3 in School Year 2015–2016, and Grades 5 to 6 in School Year 2016–2017. These programs were designed to nurture children’s social, emotional, cognitive, and physical development, enhance self-confidence, and foster a lifelong love of learning.

St. Francis High School is also a Senior High School provider, offering the General Academic Strand (GAS) and Humanities and Social Sciences (HUMSS) beginning School Year 2016–2017, and the Accountancy, Business, and Management (ABM) strand starting School Year 2017–2018.