A history tracing back to 1684, Ignacia del Espiritu Santo and her beatas started educating young Filipinas as part of their mission as a foundational community.

In 1901, the Beaterio became a congregation, eleven years after, the school was formally incorporated and the elementary and secondary course was recognized by the government.

St. Mary's College Inc. offers SHS or Senior High School with the following Academic Tracks: Accountancy, Business and Management (ABM), Humanities and Social Sciences (HUMSS), Science, Technology, Engineering and Mathematics (STEM) AND General Academic Strand (GAS).

In 1976, the changing political, socioeconomic and cultural climate led the administrators to temporarily suspend the college.

With the continuing improvement in its instruction and services, The Board of Trustees thought it was time to resume the college.