Project 3 Elementary School was first organized as an annex of Quirino Elementary School in 1953. Twelve primary classes were opened in a four-room rented building along Banuyo Street. For ten years, 1953 – 1963 it remained as an annex of Quirino Elementary School. Private houses were rented to accommodate the increasing population of the school. In 1962, five grade V classes were organized for the first time. The year 1963, marked the beginning of a complete Elementary School for Project 3 with the opening of Grade VI classes. It became an Independent Elementary School then.

The vacant Lot, 6,740 square meters adjacent to the rented school building was awarded to the school through the efforts of school officials and P.T.A. Officers. In 1964-1965, the first Pre-Fab Marcos Type Buildings in the Philippines was constructed on the lot acquired by Project 3 Elementary School. No less than the son of President Ferdinand E. Marcos, Bongbong was the guest speaker during the inauguration on August 21, 1966.

The school has gone a long way since 1953. Tremendous efforts were exerted by school administrators, SPTA, Teachers and Pupils to make the school what it is now.