Good Counsel College operates on a 2 week, 10-day cycle (Week A and Week B). Each day consists of 5 periods, each one hour in length. A bell will ring at the completion of each lesson whilst a song will play for 3-5 minutes at the end of first and second break where students are to begin moving to their next class.
The college is organised into vertical houses with four home groups, comprising of students from all year levels. Each homegroup has a home room teacher who exercises a pastoral care role, attends to roll marking and other general administrative matters. Students meet in their home groups for twenty minutes at the start of each morning.