Paco Catholic school started in November, 1912 as an informal class for 50 young boys inside the chapel in the Peñafrancia section of the district by Raymond Esquinet, CICM, who was succeeded by Fr.
Finally, the Franciscan Superior Governor ordered that the new town be called San Fernando De Dilao.
Fernando de la Concepcion Perdigon who was appointed parish priest in 1809 then started the construction of a concrete church which was completed in 1814.
In June 1913, following an increase in enrollment, Aldenhuijsen asked the Belgian Mothers (CMSA now ICM) from St. Theresa's College to help in running the school in Peñafrancia.
When Aldenhuijsen was transferred to Pasig in September 1919, Josef Billiet became the parish priest of Paco, a position he held for 10 years.
But in 1942, on the occasion of a pastoral visitation, the Archbishop of USA America insisted that at least the high school level be re-opened.
In July 1944, Josef De Bal temporarily became the school director because Aldenhuijsen, being a Dutch, was detained with other foreign nationals in Laguna.
Later Aldenhuijsen was deposed as parish priest by order of the Japanese authorities but he was reinstated on the same day through the intervention of the archbishop.
With the help of the American engineers, more repairs were made and Paco Catholic School was able to start classes in July 1945 with 1,600 students.
However, the Belgian ICM Sisters decided to withdraw their involvement in PCS, leaving their Filipino counterparts as principal of the Grade School Department.
After 72 years of dedicated service to the ministry and education, the CICM turned over the management of the school to the Archdiocese of Manila in 1984.
In 1995, the five-story San Lorenzo Ruiz Building, which replaced the Sisters' Convent that housed the Department of Religious Education or DRE, was built.
In May 1999, the construction of the Jaime Cardinal Sin Building, named after the then-Archbishop of Manila and housing 33 rooms for the high school department and a 1,000-seat auditorium started.
The structure, named after Pedro Calungsod, was blessed and inaugurated on November 8, 2002, in a ceremony coinciding with the 90th PCS Foundation Day.
Godofredo Aldenhuijsen Heritage Center following a motion and resolution passed and unanimously approved by the Parents Coordinating Board of the high school department and subsequently concurred with by Cirilos.
On the next year of January 31, 2005, the High School Department was granted the Certificate of Accreditation by PAASCU, Level I, also as approved by FAAP.
Rolando R. Dela Cruz was appointed Parish Priest and School Director, a position he served up to April 2014.
It was also under his term when the High School Department was granted with the Certificate of Accreditation by PAASCU, Level II, as approved by FAAP, in December 2010.
Beginning School Year 2012–2013, air-conditioning units were installed in all classrooms and selected laboratories to improve the learning environment.
Major changes in the Roman Catholic Archbishop of Manila Educational System (RCAM ES) were introduced in the academic year 2014–2015.
Likewise, Senior High School, as an integral part of the K to 12 Program, was established with its first batch of graduates in 2018.