The school was founded in 1932 by Fr Becheras and between 1937 to 1942, placed under the the care of Sr. Henry as Principal.
In 1985, Holy Innocents' High School (Primary Section) and Holy Innocents' Chinese Girls' School were combined to form Holy Innocents' Primary School and moved out to Lor Low Koon where it remains today.
Ponggol Convent started out in 1957 and shared it's premises with the Holy Innocents' Chinese Girls' School.
In 1999, the school was relocated to it's current site along Upper Serangoon Road. It was renamed CHIJ Our Lady of the Nativity in 2001.