A strong House system exists within the Junior School with all boys from Prep to Year 6 in a House, which allows all boys to contribute to the Academic Points award. Year 3-6 boys regularly throughout each term in their House groups. They participate in a variety of activities during these meetings and are allocated a cross age Peer Support group to work with throughout the year. The boys participate in a range of House activities that include: Chapel Services, Swimming, Cross Country and Athletics championships, Rapid Fire Cricket, Football, Soccer and T-Ball inter house events as well as House Trivia, Public Speaking and Chess.
There are four House. They are as follows:
Bradshaw - was named after the second Principal of the Junior School, D M Bradshaw. Mr Bradshaw was an Old Boy of Scotch who became Principal of Haileybury College in 1954 and later Minister of St Stephen's Presbyterian Church Surrey Hills.
Campbell - remembers H C Campbell who taught on the Junior School staff before beginning a long and successful career in the Senior School. Mr Campbell retired from the position of Vice Principal in 1967.
Healey - honours the name of C O Healey, a more recent Principal of Scotch College. Mr Healey retired in 1974 after guiding the school through a period of change and uncertainty which affected all sections of society.
Waller - commemorates the name of the first Headmaster of the Junior School. A J Waller supervised the first year of the school in Glen House in 1916 and a further twenty-seven years in the present building.