In 1946 the then Headmaster, Mr James Wilson Hogg, introduced a Junior School to the Summer Hill Campus and commenced with 36 boys in four classrooms. The Junior School, in various arrangements of classes and with up to 78 boys continued at Summer Hill until 1956, when all of the primary school boys were relocated to the Preparatory School at Strathfield.

In 2000 the Junior School was re-established by the Head Master, Mr Milton Cujes, on the Summer Hill Campus as a gesture of good faith to the families who had been committed to the Southern Campus, a venture that until this date had not been realised. The Junior School recommenced with 72 boys in four classes from Year 3 to Year 6. The classes were located in temporary accommodation between No. 1 Oval and No. 3 Oval.

In 2002 the School Council determined that the Junior School would become a permanent part of the educational profile at the Summer Hill Campus for the foreseeable future.

In 2003 the Junior School moved to permanent accommodation in the old Boarding House and was formally recommissioned in a ceremony which included Messrs Neil Buckland and Neil Demeril, both of whom had been students of the Summer Hill Junior School in the 1940s.

In 2006, the Junior School commenced operation as an Infants Campus catering for Pre-School to Year 2 students located on the previous St Thomas Becket Primary School site located in Thomas Street, Lewisham. On the 6th February, 12 students were welcomed to the school in a dedication ceremony conducted by the Head Master, Mr Milton Cujes. Prayers were led by the School Chaplain, Mr. Greg Webster and St. Thomas Parish Priest, Father Michael Butler.

The current Junior School building was opened on Wednesday 3rd October 2012.  It is a much sought after educational environment, as it is a purpose built state of the art educational building that reflects the Learner profiles of the International Baccalaureate Primary Years Programme (IBO/PYP). The IBO/PYP is a world leading curriculum framework that drives the educational pedagogy at the Junior School. The building has been specifically designed to reflect these learning principles and add depth and meaning to all learning experiences of the boys. For the first time in the short history of the Junior School, the new building will have a K-6 profile. With operable walls between pairs of classrooms, and several key break-out learning spaces, along with the Resource Centre all boys have an ideal environment as they continue their studies across the Key Learning Areas in an integrated fashion.