St. Andrew’s School was founded by Rev. Fr. Josef Van Runckelen, a Belgian priest of the Congregatio Immaculati Cordis Mariae (CICM), otherwise known as the Congregation of the Immaculate Heart of Mary. "Pare Jose”, as he was affectionately called, established the school on June 27, 1917. As parish priest, he named the school after the parish patron saint, St. Andrew the Apostle (the patron of fishermen) to whom the Augustinian friars – who established the first Catholic missions in Parañaque – dedicated the church on May 11, 1580 as aligned with the livelihood of the local residents. With the help of foreign donations from Belgium, the school was built offering the elementary grade levels (primary and intermediate) for boys and girls.

The elementary school was first housed in a modest building located across the street facing the parish church. In 1932, Fr. Van Runckelen expanded the school by establishing the High School Department, which opened to 32 co-educational students (20 boys and 12 girls). Rev. Fr. Antoon Van Overveld, CICM succeeded Fr. Van Runckelen in 1934 and two years later in 1936, due to the adversities of the times, the 32 students were reduced to seven (three boys and four girls). They were dubbed “The Magnificent Seven”, being the first high school graduates of St. Andrew’s School. Fr. Van Overveld was succeeded by Rev. Fr. Adolf Cansse, CICM in 1937. During that time the school once again opened to aspiring boys and girls. Hence, in 1938, with the growing student population, the school transferred to its present site beside the parish church, now the Cathedral Parish of the Diocese of Parañaque, across the street.

Before the onset of the Second World War, Fr. Cansse, then Director of St. Andrew’s School, invited the Sisters of St. Paul of Chartres to manage the girls’ high school education. During the succeeding years, St. Andrew’s School continued to grow and improve its quality of instruction so that by the time the Second World War broke out in 1941, it already enjoyed the reputation of being one of the best private secondary schools for boys and girls in the country.

St. Andrew’s School maintained its co-educational status until it was closed due to the outbreak of the Second World War in 1941. The school re-opened in 1945 with only the high school for boys. In 1946, the good Sisters moved to the original site of St. Andrew’s School across the street where they managed the lower grade levels for both boys and girls. It was of the agreement that upon completion of sixth grade, the boys were to move to St. Andrew’s for high school, while the girls remained in what is now called St. Paul College of  Parañaque for their high school education. In the 1950s, the Sisters of St. Paul were granted permission by the Archbishop of Manila at that time to receive only girls, while the boys moved to the school’s present location. The re-opening of St. Andrew’s School in 1945 saw its first post-war graduation four years later in 1949. Through the efforts of CICM school directors, gradual improvements in St. Andrew’s were done from infrastructure to curriculum design, which made graduates proud of their humble beginnings.

Rev. Fr. Louis Thijs, CICM succeeded Fr. Cansse in 1952 and served as the Director of St. Andrew’s School until 1977. In 1969, Rev. Fr. Paul Foulon, CICM, another Belgian priest who was the High School Principal from 1964-1966 became the Assistant Director and School Director of St. Andrew's School up to 1977. He succeeded Fr. Thys to become the School Director until 1991. Rev. Fr. Frans Gevaert, CICM was the last CICM priest to have assumed the directorship of St. Andrew's School from 1991 to 1993 due to the turnover of St. Andrew’s School from the Religious to the Diocesan administration of the Archdiocese of Manila in 1994.

During the turnover in 1994, Rev. Fr. Romerico A. Prieto became the first Diocesan School Director of St. Andrew’s School followed by Rev. Msgr. Manuel Sebastian who took over the same position from 1995 to 1996. Rev. Msgr. Bayani G. Valenzuela succeeded Msgr. Sebastian from 1996 to 2004. In 1999, the school established the Preschool Department, which was the result of the collaborative efforts of Msgr. Valenzuela and Mrs. Gertrudes Bautista. In 1999-2000 started the enrolment of female pupils in the preschool, who proceeded to the elementary and high school grade levels as the years ensued. Thus, St. Andrew’s School had once again assumed the status of a co-educational school after many decades of being an exclusive school for boys.

The directorship of Msgr. Valenzuela paved the way for the general face lifting of St. Andrew’s School, to wit: the construction of the new building that houses the preschool and elementary classrooms, the Instructional Media Center, computer laboratories, science laboratories for Physics and Chemistry, and the Home Economics room. It was also during the same term when the construction of the audio-visual room, multi-purpose hall and gymnasium, and the renovation of the administration and faculty offices took place.

Year 2003 marked the birth of the Diocese of Parañaque with His Excellency Most Rev. Jesse E. Mercado, D.D. as its first bishop. As such, the SAS administration was assumed under the jurisdiction of the new diocese. School Year 2004-2005 welcomed Rev. Msgr. Manuel G. Gabriel who succeeded Msgr. Valenzuela. Under the direction and guidance of Msgr. Gabriel, the Vision, Mission, Goals, and Core Values of the school were formulated in keeping with the missionary spirit of the school’s forefathers; the organizational structure was also revised.

School Year 2005-2006 gave birth to the Center for Early Childhood Education (CECE), which is a three-year preschool program that enrolled children aged three to six years. The Center for Early Childhood Education eventually evolved into the present Primary Grade School Unit of the Integrated Basic Education Department (IBED) of St. Andrew's School. In subsequent years, two more academic programs were established, namely, Special Education (SpEd) and the Alternative Learning System (ALS) and Skills Training and Development programs, both under the IBED.

In School Year 2010-2011, the school once again transitioned into the new developments of the Philippine Basic Education system. The Department of Education gradually introduced the new K to 12 Enhanced Basic Education Curriculum, which necessitated major adjustments in curriculum implementation and student assessments. Hence, with the assumption into office of Rev. Fr. Rolando R. Agustin, who succeeded Msgr. Gabriel in 2012, the office of the Institutional Principal, then headed by Rev. Dom. Gerardo Ma. de Villa, OSB (2014 - 2018), was created in order to assist the School Director in the administration and management of St. Andrew's School.

In preparations for the 500 years of Christianity in the Philippines (2021) and as post-centennial director, Rev. Msgr. Allen C. Aganon (2018 – 2020) expanded, innovated and transformed the school into a 21st century learning hub. As a prime mover to new heights in facilities and physical structure, it continues to showcase Science, Technology, Engineering and Mathematics (STEM) - Robotics to students. Msgr. Aganon was assisted during his term by two Diocesan priest namely, Rev. Fr. Roderick S. Pacoma as the CIE Head and Rev. Fr. Enrico S. Salazar as the Administrative Services Head. Mr. Lord Celeste E. Balo (2018 - present) was promoted as the Institutional Principal of the Basic Education Department.

In year 2020, the Diocese of Parañaque Parochial Schools Association, Inc. (DOPPSA) Superintendent, Rev. Fr. Augusto C. Pulido (2020 - present) became the School Director of the institution. During his term, Fr. August Pulido faces a worldwide challenge in education - the COVID-19 pandemic. St. Andrew's School made a bold move by means of working together in the New Learning Environment in education. Online Distance Learning - Synchronous and Asynchronous Learning was implemented as learning modality in the new normal education of students.

As the oldest parochial school in Parañaque, St. Andrew’s School has been known to deliver quality and relevant Catholic education to the youth, heeding the call to serve love and excellence through its curricular and co-curricular programs including outreach and community service, pro Deo et patria!