The museum was first established in the year 1965 by Rev. Fr. Ambrosio J. Galindez, O.S.A., mainly for the purpose of commemoration of the fourth Centennial Celebration of the Christianization of the Philippines. It was located at the Basilica Minore del Sto. Niño de Cebu Convent. Vestments and assorted offerings to Santo Niño were displayed in a certain room at the convent.
At present, the museum is located at the basement of the Santo Niño Pilgrim Center which was completed in the year 1995. Due to the increasing number visitors and devotees, and all collections as well, the Augustinian community moved the museum to a more spacious area. The main objective of the museum is to make people aware of the origin, circumstances and events related to the formal Christinanization of the Philippines through the image of Señor Santo Niño de Cebu.
