The Middle School at Aquinas College caters for boys from Year 7 (2010) through to Year 9 and becomes a transition from the primary school years through to secondary. It matches boys' developmental progress with appropriate activities for boys going through this stage of their lives.

Boys are able to develop and grow in an environment that is structured with strong pastoral emphasis to nurture their independence and resilience. There are a breadth of academic activities to engage boys in their learning and enable them to explore a diversity of offerings. The curriculum provides a foundation for learning, with technology being a significant element in content delivery.

In the initial stages of Middle School boys have a set program so they are able to make decisions on future subject selections based on their own experience. There is a range of options for boys to take as they progress through the Middle School so that interests can be followed.