The history of the school can be traced backed in 1959 when Mother Maria Valentina Ayerra of the Servants of St. Joseph, then superior of the Holy Family Dormitory-Manila, procured a lot that would be later used for Holy Family School. The nuns from the Servants of St. Joseph later started the construction of the school in 1966 in three phases and was completed in 1971. The operations of the school began on July 1966 with a class of 50 students, both boys and girls. Two rooms were used which were the facilities available for use at that time. Boys were admitted for the pre-school level until the practice was discontinued in the mid 1980s due to limited number of classrooms and the school administration prioritized admitting female students. Due to the growing student population from 1967 to 1975, the Novitiate which stayed on the top floor of the school building transferred to a small house within the compound of the school. Another house was built in 1975 to accommodate working girls and some of the faculty members. In 1981, The Novitiate transferred to Tandang Sora when the Servants of St. Joseph nuns moved into the house they previously occupied. During its early years from, Holy Family School established the Holy Family Clinic and Holy Family School Branch which primarily served Barrio San Vicente. The school also sent selected fourth year students to Pinyahan Elementary School to give Catechetics. For two years in a certain period of the school's history, that the school offered Vocational Course related to dressmaking. From 1985 to 1989, the school provided free late afternoon classes for working high school students both male and female and other students from poor families. As part of the celebration of the Silver Jubilee of the school in 1991, the Educational Assistance Program which gave scholarships to poor students who were deemed deserving by the school was revitalized and expanded. The program lasted for two years which included Shop Class and Income Generating Projects. The school underwent a reorganization which includes making amendments to its Vision-Mission in 1993 and in 2008-2009.
