There are six houses, some are named after persons who have contributed to Masaka Secondary School.
All Students are placed in a house when they are admitted into the school and they are expected to participate in all activities of the house.
The Houses are:

1. Kenyatta House.

2. Africa House.

3. Lumumba House.

4. Agakan House.

5.Nile House.

6. Kerr House.