CSFJ has been through many renovations lately, and added various buildings which are helpful to the quality education of which the school promises.

Colegio de San Francisco Javier, formerly Xavier High School was born out of the municipality of Rizal's pioneering settlers' desire to get their children secondary education without sanding them away to the city or other places. These religious and civic-minded citizens thought a Christian education would be ideal for their children and for all the coming generations. On February 3, 1950 Rev. Fr. Ubaldo C. Basoc, the first parish priest of Rizal and founder of the school, applied for a permit to open first and second year levels of academic secondary course. The administration and the Board of Trustees received the approval to use the 1.6 hectares of public land for the school site and built three classrooms for the first 100 high school students. The permit was approved by the Bureau of Private Schools in April 1950 to start its school operation in July 1950. On its third year in operation (1953), School Director Fr. Ubaldo C. Basoc requested the religious sisters to run the school from the very Rev. Mother Maria Andrea Montejo, Superior General of the Religious of the Virgin Mary. She sent Rev. Sister Ma. Agatona Gomez as the Superior to manage the school with Sister Ma. Lorenza Tabiliran and Sister Ma. Margarita Queveda. The RVM sisters fulfilled the desire of Fr. Basoc to make Xavier High School as an active catalyst in religious activities and in the Christian formation not only of the students but also of the people of the community. Xavier High School saw a succession of mother superiors, three of the longest assignments were those of Sister Maria Sinforosa Ravina, Sister Maria Winifreda Asok and Sister Maria Erlinda Cabilin. To accomodate the population growth, a new bigger school building was completed in 1964.