Balwyn High School's house system was established in the second half of 1954. The school’s historical records explain that:
For sport and other purposes the school has been divided into four houses equal in number. Because our school was founded in the Royal year, we have called these houses Windsor, Edinburgh, Strathmore and Churchill. Each house has adopted a distinctive colour and these will be worn at all inter-house games and contests.
This tradition has been preserved and maintains a high standard of competitive spirit among students.
The House System encourages competition in many areas such as swimming, athletics ,debating, music, subject-based competitions and fun raising talent quest.
The House Cup is presented to the captains of the winning house at Presentation Night each year.