In February 1974, Msgr. Jose Flores established the Holy Family Parochial School, commencing its educational journey with 33 kindergarten pupils under the guidance of the Good Shepherd Sisters. The administration baton was later passed to the Daughters of Mary Leuca from 1975 to 1979. Notably, in 1979, the school attained official government recognition for providing comprehensive Elementary Education, marking a milestone with an enrolment of 158 pupils. The school began academic supervision by a lay administrator in 1979-1980, and Magdalena B. Queppet served as the School Principal from 1981-1984.

Priscilla M. Cembrano acted as the School Principal for the school year 1984-1985. In 1985-1986, the school opened the secondary level, Ruben Dela Fuente, Marissa T. Verzosa, and Magdalena B. Queppet acted as School Principals succeedingly. The secondary level lasted only for three years from 1985-1988 due to compliance issues with government requirements. In June 1988, Msgr. Jose Flores transferred to a new assignment, and Rev. Fr. Gaudencio Salise was assigned as the Director for six consecutive years from 1988-1994. In 1994-1995, Msgr. Marcelino Reyes took over as director for one year.

Rev. Fr. Reynaldo Bungay was the Director from 1995-1999. Mrs. Loretta P. Pantoja served as the School Principal in the year 1989-2000, and in 1997-1998, the school faced a decline in enrolment and was considered for closure. Despite this, the school continued to operate. In 1998, the Board of Trustees decided to close the school by the end of the 1999-2000 school year, but Rev. Fr. Romerico Prieto’s five-year plan and recommendation to continue operations led to the revocation of this decision. The school underwent major renovations in infrastructure and teacher development training in 2000-2001. In 2002-2004, Mrs. Sonia D. Madrid served as the School Principal.

In 2004-2005, the secondary level was reopened under Mrs. Nenita M. Naniong as School Principal until 2007. Rev. Fr. Joselito M. Irlandes was appointed as the school director from 2006-2012. During his term, a four-storey building was constructed to house the secondary level, which was blessed by Bp. Honesto Ongtioco on November 6, 2010. In 2008, HFPS received certification from the Department of Education (DepEd) through the Fund for Assistance for Private School (FAPE) to accept learner grantees under Education Service Contracting (ESC). In 2012, Rev. Fr. Raymond Joseph L. Arre was appointed as School Director, and Mrs. Ciel Katherina M. Acacio as school principal. The school implemented the K to 12 Basic Education Program for Grade One and Grade Seven during this time. A new vision and mission were established for the school in 2013-2014.Likewise, it was this year when the Diocese of Cubao Education System, Inc. (DOCES)  began to supervise the school with Rev. Fr. Raymond Joseph L. Arre as the Superintendent. The school employed the Dynamic Learning Approach in June 2015 and received re-certification from DepEd FAPE-PEAC in September 2015.

Annually, the DOCES General Assembly was organized leaving a significant milestone. In 2017, the DOCES Parochial Schools Month was inaugurated. Transitioning to 2018, the appointment of Mr. Ferdinand G. Garcia as the Officer-in-Charge Principal in January marked a pivotal leadership change. In the Academic Year 2018-2019, the school’s Board of Trustees chaired by the Most Reverend Honesto F. Ongtioco D.D. approved the swapping of the High School Building and the parish rectory as agreed upon by the school and the Holy Family Parish, represented by Rev. Fr. Ron Mariano Roberto, Parish Priest. The renovation of the new building was made possible with the efforts of the Diocese of Cubao Educational System Superintendent and School Director, Rev. Fr. Raymond Joseph L. Arre with the support of the school’s education partners.