After World War II, the site served as a grazing ground for carabaos. It later became a parking area for carts transporting parishioners from remote barangays for Sunday Mass. At its center stood a concrete gazebo, where the Catholic Hour was held weekly. The priest led opening prayers, followed by catechesis from leaders of various religious associations.

In 1964, under Parish Priest Msgr. Bonifacio Boaqueña, D.P., a bamboo and nipa cottage was built for Caton classes for children. He named it Pili Catholic School and invited Ms. Leticia Postigo to teach. In its first year, the school had 24 students.

When Msgr. Boaqueña’s term ended in 1977, Ms. Postigo continued to teach and named it Santo Niño Kindergarten School after she received an image of the Santo Niño from Msgr. Boaqueña in recognition of her free services.

When Msgr. Arellano became the first Bishop of the Diocese of Libmanan, Msgr. Noriel Priela succeeded him as Parish Priest. He renamed the school St. Raphael Christian Formation and Learning Center and added a kindergarten level. Responding to the growing demand for Catholic elementary education, Msgr. Priela built four concrete classrooms and applied for a permit to operate as a formal primary school.

The Department of Education, Culture and Sports approved the permit to operate, and the school was renamed Pili Parochial School with its own official seal. By School Year 1999–2000, all grade levels were complete, and the first graduation under the name Pili Parochial School was held in March 2000. Msgr. Priela also constructed a building on the left wing to house nursery and SPED classes. He remained dedicated to the school’s development and continued to lead it until his passing on December 4, 2001

Msgr. Pablo Aguilar’s term is remembered as the Golden Age of Pili Parochial School. He oversaw the construction of the right-wing building and began work on the Administration building, though it remained unfinished due to his untimely passing. Under his leadership, enrollment peaked at 463 in 2002 and remained steady through 2009.

Msgr. Jesus Picar took office on November 7, 2008, after Msgr. Aguilar’s passing. He completed the Administration Building and began the perimeter fence, but enrollment declined due to rising private school competition and economic hardship. In 2016, Fr. Lorenzo Jarcia, a talented musician, became principal, rearranged the school hymn into a marching tune, introduced a Special Education Program, and revised the school seal. Despite these efforts, enrollment kept dropping. Fr. Jarcia used personal funds and Archdiocesan loans to sustain operations. Both leaders made significant contributions while facing persistent challenges in maintaining student numbers and financial stability.

In early 2020, just as recovery efforts took hold, the COVID-19 pandemic struck. Undeterred, Fr. Tria revised the school’s vision, mission, and seal with community input. Graduation rites were held at students’ homes due to lockdowns. In June 2020, Fr. Enrico Julian Paglinawan became the school’s first appointed principal. Through house-to-house visits, altar server recruitment, and parishioner support, enrollment steadily grew. While many schools faced declines, Pili Parochial School’s population doubled each year. In 2021, the Department of Education granted permits to open Grades 9 and 10, as well as Senior High School under the General Academic Strand.

In 2022, with the support of the Engineering Department of the 9th Infantry Division of the Philippine Army, two old and dilapidated classrooms were renovated and transformed into the school’s new library. This project marked a significant step in improving learning resources and infrastructure, made possible through strong community partnerships. The renovation not only preserved space but also promoted a culture of reading and academic support within the school.

In 2023, the school expanded its Senior High School program by opening new strands: Accounting, Business, and Management (ABM); Humanities and Social Sciences (HUMSS); Science, Technology, Engineering, and Mathematics (STEM); and the Arts and Design Track. The same year marked a major milestone—the first Senior High School graduation, with 32 pioneering students receiving their diplomas. This growth reflected the school’s commitment to providing broader academic choices and preparing students for college and future careers.

In 2024, in response to Pope Francis’ call for inclusive education, the Board approved the school’s transformation into a Higher Education Institution. On January 16, CHED granted the permit to offer a Bachelor of Special Needs Education (BSNED). DepEd also approved the addition of the Technical-Vocational-Livelihood (TVL) strand for Senior High. In February, the SEC issued the amended articles of incorporation, officially renaming the school to Colegio de San Rafael Arcangel, Inc. (CSRA). By May, the school was certified by PEAC as an ESC Program implementer, ensuring government subsidies for Grades 7–10 for the next three years.

CSRA envisions expanding its college programs, building student dormitories, and enhancing facilities to better serve the youth. With a strong commitment to faith, service, and academic excellence, it aims to become the leading Catholic Higher Education hub in the province. Guided by its mission to form Christ-centered, competent, and compassionate individuals, the school remains dedicated to making quality Catholic education more accessible to all, especially the underserved communities.