The school was founded in January 2007, having been brought into existence through the efforts of an interim Board which had the vision to provide an affordable Christian school striving for excellence in education, for the families of the Mornington Peninsula.
Balcombe Grammar School is a co-educational Foundation to Year 12 school governed by a Board of Directors and managed by a Consultative Committee. Members of these two bodies include representatives from churches, parents, individuals with specific expertise, the Business Manager and the Principal. It is operated by a company limited by guarantee.
The school is a member of the Victorian Ecumenical System of Schools (VESS) which comprises eighteen schools throughout Victoria and is also a member of Independent Schools of Victoria (ISV).