Sto. Niño Elementary School began in 2001 with the construction of a modern two-storey, six-classroom building on a lot owned by the National Housing Authority. The project was undertaken by the City Government of Pasig under the administration of City Mayor Soledad C. Eusebio. The building was inaugurated on November 23, 2001, in preparation for School Year 2002–2003.

The school opened with 242 pupils from Grades One to Six and six teachers. As enrollment increased, additional classrooms and facilities were constructed, including the Soledad C. Eusebio (SCE) Building 2 in 2004, the Vicente P. Eusebio (VPE) Building in 2005, and the Robert C. Eusebio (RCE) Building in 2019.

Formerly known as Dela Paz Elementary School–Annex, the school gained independence from its mother school on August 30, 2005, and was officially renamed Sto. Niño Elementary School through City Ordinance No. 11, s. 2005. The name, chosen by Mrs. Soledad C. Eusebio, pays homage to the Sto. Niño (Holy Child Jesus) and reflects the values of faith, hope, and guidance.

From its humble beginnings, Sto. Niño Elementary School has continued to grow and develop, remaining committed to providing quality education and serving its community with dedication and excellence.