St Francis Xavier runs a School House system that spans key stage 3 and 4. There are 4 Houses named after important Abbeys in the area, Jervaulx, Easby, Rievaulx and Fountains. 

The Houses are used within the day to day running of school life and as part of the Behaviour and Reward system.

The Houses compete through a series of initiatives including the merit system, subject specific competitions, cross-curricular challenges and sporting activities. They are also used to support the many charitable activities the children and staff undertake to raise funds for good causes here and abroad.

The ultimate challenge in the House calendar is School Sports Day where pupils take part in a range of sporting events to gain points for their respective Houses. The House with the most points at the end of the academic year is awarded the House shield in school assembly and milestone rewards are given during the school year including early lunches, film parties and treats.

The House system is designed to encourage all pupils to feel the benefits of becoming actively involved in school life; sharing a common goal with children in different age groups whilst offering an additional system of support and development by rewarding positive behaviour.