St Martin’s School prides itself on the traditional prefect body system of leadership. The Preparatory School is led by a head boy and head girl, deputy head boy and deputy head girl, and prefects. Prefects are allocated to mentor classes throughout the school. Heads of Houses (Founders, McGregor and Pioneer) – not necessarily prefects – are chosen to lead their houses during inter-house sporting events. Servers are on duty during church services and, together with library monitors, complete the leadership structure of the school. Two learners are elected to the Johannesburg Mini City Council.

In the High School, the school is led by heads of school, usually a Head boy and Head girl, deputy Head boy and deputy Head girl, the heads of Houses and a prefect body.