In 1953, parents of the Catholic Chinese Community of Cebu City approached Fr. Paul O'Brien, then the Superior of all the Jesuits belonging to the former missions in China, requesting him to supply manpower for the establishment in Cebu City of a middle school for the education of their children.

   The Fathers of San Jose Recoletos generously gave the new school legal status by affiliating it with their school and by providing it with their Principal and a contingent of lay faculty members.

     In 1955, Sacred Heart School was established as an independent school.

    On 25 Febuary 1965, Sacred Heart School became a Filipino School, approved by the Bureau of Education to teach the regular curriculum prescribed by the government with a Chinese Language and Arts program.

    In December 1988, Sacred Heart School was integrated into the Jesuit Philippine Province together with Xavier School in San Juan and Santa Maria in Iloilo.

    Aside from its emphasis on religious and moral formation, academic excellence and personal discipline, Sacred Heart School of the Society of Jesus also serves as a bridge between the Filipino and Chinese-Filipino communities through Christian education that aims to form graduates characterized by "Christian witness, effective chitizenship, service and leadership."