The organizational chart of Sto. Niño Parochial School, Inc. illustrates the school’s governance and management structure. At the top are the Board of Trustees and the Superintendent, supported by the Deputy Superintendent and Superintendent’s Council. The School Director oversees the Administrative and Educational/Legal Councils, as well as the External Auditor.

The school’s operations are divided into five main centers: Christian Formation, Student Services, Teaching Learning & Assessment, Administrative Services, and Finance Services. Each center is led by a head and includes various departments and coordinators to ensure effective delivery of educational, spiritual, administrative, and financial services. This structure supports the school’s mission of forming faith and building the future, with faculty and students at the core of its community.