Academia de San Martin (formerly: Saint Martin de Porres Academy Inc.) was founded by His Eminence the Lord Cardinal Julio R. Rosales on 03 June 1968 as an answer to the petition of parishioners and in honor of his favorite saint. The first batch of Daughters of Charity arrived in Daanbantayan on 27 June 1968: Sr. Dolores San Miguel, Sr. Marcelina Lignig and Sr. Rosella Pandong. They first stayed in a private house for a week until they transferred to a house rented for them by the Parish Pastoral Council on 03 July 1968.

The school founder officially designated the Daughters of Charity of St. Vincent de Paul as the administrator of the new learning community on 08 July 1968. Government recognition for the complete secondary curriculum was granted on 03 September 1974. Colegio de la Inmaculada Concepcion, Cebu City provided valuable assistance leading to the construction of a two-storey concrete school building in 1981. Slowly but surely, the school continued to grow and develop as an educational institution.

In 2003, Sr. Zenaida S. Condes, DC served as the Central and Eastern Visayas Cluster President. Under her stewardship, Academia de San Martin enjoyed certain benefits and privileges as member of the Daughters of Charity-St. Louise de Marillac Educational System. In 2009, the academy became a supervised school of Colegio de la Inmaculada Concepcion, Cebu City. In 2012, Academia de San Martin implemented the K to 12 Basic Education Program. In 2015, the plan to turn over the school to the direct administration of the Archdiocese of Cebu was presented by Sr. Maria Ana Rosario G. Evidente, DC, the Visitatrix of the Congregacion de la Compañia de las Hijas de la Caridad de San Vicente de Paul en las Islas Filipinas to His Grace Archbishop Jose S. Palma, SThD, DD. The Office of the Superintendent of the Archdiocesan Catholic Schools of Cebu System was empowered by the Roman Catholic Archbishop of Cebu to facilitate the transition process.

On 28 April 2017, Academia de San Martin was formally integrated into the Archdiocesan Catholic Schools of Cebu System with Fr. Jesper John R. Petralba, EdD, DM, PhD, DPA as the first ex officio School Director and Fr. Josephus C. Remonde, MAPM as Principal-Treasurer. During the second semester of SY 2017-2018, Fr. Jestoni T. Del Castillo, M.A.P.M. and Fr. Mariano Dioscoro E. Cuarto, M.A.S.L. were designated as School Principal and School Treasurer respectively. The triumvirate commendably animated the Golden Founding Jubilee Celebration of the learning community on 03 June 2018 while decisively addressing backlogs in regulatory compliance. A service vehicle was acquired through the generosity of Academia de San Isidro Labrador. In 2019, Fr. Jestoni T. Del Castillo, MAPM was appointed Principal-Treasurer. This learning community remembers the past with gratitude, celebrates the present with joy and anticipates the future with enthusiasm.