The school population is divided among four houses. Young women entering in Form 1 are placed into a house according to their place in the roll. The first person on the roll is placed in blue, the second in yellow, the third in red, and the fourth in green etc. Often, young women request the house in which a relative was a member while they attended SJCSJ.
Each house is led by a Captain and assisted by a Vice-Captain. There are also two young women who serve as Head Girl and Assistant Head Girl. Also introduced later on was Sports Captain and Assistant Sports Captain.
All captains and assistants would usually be in Form 6.
The four houses are:
- Mary Immaculate Queen - blue - often called MIQ. It is named for Mary, mother of Jesus of Nazareth
- Saint Joseph - yellow.
- Saint Maria Goretti - red - often called SMG or Maria Goretti.
- Blessed Anne Marie - green - often called BAM or Blessed Ann.