Our school began as the 'Bunnerong School of Our Lady of the Rosary' in 1907 on the land which is now Perry Street in Matraville.

The modest timber school-church was officially opened and blessed by Archbishop Kelly on 20 January 1907 and commenced its first school term with 52 students.

At the time, the school was located in an underdeveloped area with few permanent homes. The one-room school catered for children of itinerant workers who lived in the surrounding sandhills and who were too poor to educate their children. Although providing ample space for the children to play, the school grounds were primarily sand, with a little creek running at its side.

The Sisters of Our Lady of the Sacred Heart from Botany conducted the school.

On 6 November 1949, the foundation stone of the new school building in Perry Street was blessed by Cardinal Gilroy and, with substantial assistance from the local parish community and parents, the building was completed on 2 May 1951. The new school building also served as the church until a new church could be built.

In 1956, the Church secured title to a vacant block of land on Bunnerong Road with the intention of constructing a new and modern central school building.

The vacant land was originally a sandstone quarry which had provided materials to build roads throughout Sydney.

With the support of the local parish community, construction of the school was completed in June 1958 and the new building was officially opened and blessed on 26 October 1958 by Cardinal Gilroy.

Parish Priest Father James Munday planned to expand St Agnes' School by purchasing additional land, adding further buildings for the school, and building a separate church.

In January 1966, St Agnes Church was blessed and opened, enabling those buildings designed for the school to be used exclusively as classrooms.

In 1981, the OLSH Sisters withdrew and the first lay Principal was appointed.

In 2009, the stimulus grant from the Federal Government's 'Building the Education Revolution' initiative allowed work to be undertaken to completely refurbish the library into a multipurpose learning area, infants classrooms to be upgraded, the hall to be renovated into a modern facility and undercover walkways and disabled ramps to be installed.

This extensive refurbishment allowed St Agnes' to continue to provide a high standard of education, taking all learners into a 21st century learning environment.