The curriculum at Mount Lilydale Mercy College is organized into three phases:

·        Year 7 Transition Year;

·        Years 8 -10 Core homeroom and Non-core mixed groupings; and

·        Years 11-12 Victorian Certificate of Education (VCE)

·        Years 11-12 Victorian Certificate of Applied Learning (VCAL), incorporating Vocational Education and Training (VET) programs.