Academia de San Pedro Calungsod (formerly: Siena School of Naga) was founded by His Eminence the Lord Cardinal Julio R. Rosales in 1965. He appointed the Congregation of the Dominican Sisters of Saint Catherine of Siena as its chief steward.

The co-educational school started its operation with only Kindergarten and the first two years of high school as initial offerings. First Year and Second Year Secondary courses received government recognition in 1966. The Third and Fourth Years Secondary courses gained government recognition in 1967 and 1968 respectively. Despite financial difficulties the fledgling institution of learning managed to survive with the grace of God.

School Year 1984–1985 witnessed the considerable growth of the school population. The trend continued progressively until 1996. The construction of the Saint Dominic Building became necessary.

The Preschool Education was closed in 1994 due to dwindling enrolment. The following year, the construction of the Saint Martin Building and the Mother Francisca Outreach Building, where the chapel, clinic and pupil/student services offices were housed, was completed.

Due to economic and managerial factors, the downtrend in terms of enrolment began in 1996. Despite the unprecedented predicaments, the school renewed its commitment to quality Catholic education with the help of its competent and loyal human resources.

And so in response to a felt community need, the school reopened the Nursery and the Kindergarten Courses in the School Year 2000 – 2001. The move earned government recognition in 2003. The following year the concrete fencing of the school was accomplished. The school also pursued renovation projects to improve educational facilities through the generosity of the Parents-Teachers Family Council and the Alumni Association.

Towards the end of 2004, the Educational Service Contracting (ESC) Certifying Team from FAPE (Fund Assistance for Private Education) Regional Office and the Department of Education (DepEd) Regional Office evaluated the school in all areas of operation and rated the school as one of the excellent schools in Cebu Province.

In the same year the Saint Dominic Building was pronounced unfit for occupancy by the Office of the City of Naga Engineer due to substandard materials. It was eventually demolished for safety and security purposes.

In School Year 2005 – 2006, the Congregation of the Dominican Sisters of Saint Catherine of Siena considered a possible merger between the two congregation-run schools in Cebu: the Holy Rosary School of Pardo and the Siena School of Naga, but it did not work out.

Another ESC-Educational Voucher System (EVS) Certifying Team from FAPE Regional Office and DepEd Regional Office evaluated the school in all aspects of operation in December 2008 and gave the school a rating described as practicing the minimum standard to a great extent.

In June 2009, the Preschool Department was closed again because of drastic ebb in population. The school was considered by the Congregation of the Dominican Sisters of Saint Catherine of Siena a mission or subsidized school in 2010 due to its depleted financial resources.

In 2011, the custodian of ASPC for more than four decades turned over the only Catholic school in the locality to the Archdiocese of Cebu through the Very Rev. Eduardo O. Ventic, PhD, Superintendent of the Archdiocesan Catholic Schools of Cebu.

Without delay, the Roman Catholic Archbishop of Cebu, His Grace the Most Rev. Jose S. Palma, SThD, DD appointed the first diocesan priest-administrators on 20 May 2011: Fr. Christopher C. Amores, MAPM as School Treasurer and Fr. Jesper John R. Petralba, EdD, DM, PhD, DPA as School Director-Principal. The following year Fr. Conrado C. Sedillo, Jr., DM was appointed by the Roman Catholic Archbishop of Cebu as Principal-Treasurer.

Just a few months into their educational ministry, the new administrators with the blessing of the newly constituted Board of Trustees implemented a new organizational set-up responsive to the demands of academic excellence characterized by a strong Catholic trademark and by a commitment to high order learning for all.

In response to a communal clamor, the new administration animated the process leading to the re-opening of the Preschool Education Course and the opening of the Elementary Education Course and their consequent government recognition in 2014. The administrative, faculty, staff and pupil/student manuals were also revised. The foundations of the Senior High School Program were properly laid.

A Jubilee Building was inaugurated and blessed on 21 October 2015 to commemorate the school’s 50 years of committed service in the vineyard of Catholic education. In 2016 the Board of Trustees decided to extend the corporate life of the school and to give it a new name: Academia de San Pedro Calungsod. San Pedro Calungsod de Cebu was designated as the school’s patron and titular.

In 2017, Fr. Venedict R. Into, MAPM became part of the administrative team. A year after that, technology-aided instruction was pursued and the ten-classroom Centennial Building was inaugurated and blessed on 24 July 2018 in celebration of the 100 years of Marian Apparitions in Fatima. A Monument of Devotion was inaugurated and blessed on 21 March 2019 in anticipation to the Quincentennial Celebration of Philippine Christianity. In that same year, Fr. Dindo C. Yosores, DM and Fr. Jerald N. Pinay, DM were appointed Director-Principal and School Treasurer, respectively.

The school year 2020-2021 was very crucial when the pandemic brought by Covid-19 greatly affected the school, yet it remained steadfast amidst the challenges and crisis as it gradually adopts, even before the pandemic, to the new normal way of the teaching-learning process. In 2021, Fr. Conrado C. Sedillo, Jr., DM and Fr. William B. Alcalde, MAPM were appointed School Director and Basic Education Principal, respectively.

The story of Academia de San Pedro Calungsod is the ongoing manifestation of God’s generosity working through selfless human initiatives. It is the never-ending proclamation that miracles do happen as long as there are people of goodwill.