Sto. Niño Kiddie School was established as a Preschool in 1982 at Biñang 2nd , Bocaue, Bulacan by Mrs. Gloria Yulo Lazaro and her family. The school started with two classrooms and 70 pupils. After two years, Grade 1 was organized, and the name was changed to Sto. Niño School. The first Elementary Commencement Exercise was held in March 1991. In 1995, the school held its First Commencement Exercises for the Secondary level.
In 2002, Sto Niño Academy established its first branch in San Rafael, Bulacan – Sto. Niño Academy of San Rafael (SNA SR) to cater to the students in the northern part of the province. SNA SR held its first Commencement Exercises for the Secondary level in March 2012.