The school operates a house system and at the start of the pupil's time at St Margaret's,  they become a member of one of the four houses named Sapphire, Ruby, Emerald and Topaz. House points are awarded for a variety of reasons such as good work or behaviour, for special achievements or to encourage pupils. There are also opportunities for houses to compete against each other over the course of the year, culminating in Sports Day.

House Captains are appointed from Year 6. Each Friday, house points earned by each house are collected and the results shared in Shine Collective Worship. At the end of the year, the house with the most points is awarded the School Cup.