The College is organised around three Houses - Fitzroy, McCormack and Penola. Each House has approximately 185 young women from Year 7 to Year 12. Seven House groups make up each House and are the primary pastoral groups for the young women. Each young woman usually stays in the same House Group with the same House Group Teacher and Head of House (where possible) for her six years at Mary MacKillop College.
Houses meet fortnightly at their respective House Assemblies to celebrate students' successes, to acknowledge individual and House achievements and to plan activities which enable the young women of the House to live out their House values. Each House is led by two House Captains who role model both College and House values through their leadership.