There are four houses in the Lenzie Academy House System with each House named after notable Scots; Fleming, Inglis, Mackintosh and McKay. Each House is made up of 2 guidance groups and is represented by a colour.

Fleming – groups DM and MC (red)
Inglis – groups MB and WR (yellow)
Mackintosh – groups RA and SL (green)
McKay – groups CN and MH (blue)

The Interhouse competition runs throughout the year and the winners are awarded the PTA (FOLA) House Cup at the annual prizegiving. Each House is led by two House Captains who are supported by a staff House Leader. Senior House Teams are responsible for organising charity events and interhouse competitions both curricular and extra curricular. Pupils can win points for their House by participating in these events and by demonstrating good attendance and behaviour.