On September 20, 1954, Mary the Queen Personal Parish for the Chinese was created by His Excellency, Msgr. Rufino J. Santos, Archbishop of Manila, by virtue of the faculty granted to him by the Sacred Roman Consistorial Congregation (July 23, 1954). The parish chapel was located at 2437 Zamora Street, Pasay City. The personal parish had the following limits: "In the north, boundary line of Manila and Quezon City, towards the Marikina river in the east, running down to the southern towns of Rizal, comprising San Juan, Mandaluyong, Pasig, and Makati; down the boundary lines of Cavite and Laguna provinces. All the Chinese inhabitants will constitute the members of the New Parish." At that time, Fr. George Etienne Beauregard, S.J. was appointed the first parish priest (November 24, 1954), while Fr. Luis Chia, S.J. was appointed the first assistant parish priest (May 1963).

In the year 1963, the Jesuits were able to purchase a few hectare of land in Little Baguio, San Juan for the purpose of transferring here the Xavier School from its previous location at Echague, Quiapo. A 5000 square meter lot was allocated also for transferring the Mary the Queen Church from its original location at Pasay City. On May 31, 1963, His Eminence, Rufino J. Cardinal Santos, blessed the cornerstone of the new church situated between Xavier School and Immaculate Conception Academy in Little Baguio, San Juan. After two years of construction, the Mary the Queen Church was finally opened to serve the faithful on May 31, 1965 with the blessing of again His Eminence Rufino J. Cardinal Santos.