Highlands Christian College is part of the corporate structure of Highlands, which is incorporated by Letters Patent under the Religious, Educational and Charitable Institutions Act (Queensland).

According to its constitution, the governing body of Highlands (previously Christian Outreach Centre) is the Oversight Committee. However, the constitution provides that management of local church affairs is in the hands of the local church Committee of Management.

The local church has delegated the responsibility for the governance to a College Board appointed by the church.

The College is a member of Associated Christian Schools and the Association of Independent Schools of Queensland.