The College Council, governing body of the College, is made up of two entities, the Proprietors Trust Board and the Board of Trustees.

The Lindisfarne College Proprietors Trust Board was founded in 1953 for the original purpose of providing a Presbyterian Christian education for boys from Form 1 to Form 7.

The Trust Board is an independent body with power to appoint its own members who must be approved by the General Assembly of the Presbyterian Church Aotearoa New Zealand . The Trust is incorporated under the Charitable Trusts Act 1957 (previously the Religious Charitable and Educational Trusts Act 1908) and 2005 .

In 1999 the Proprietors gained approval from the Government to become a state-integrated school.  The integrated school is governed by a Board of Trustees (BOT) consisting of five parent elected members, the Rector, one student, one staff representative and four proprietor nominees.  Elections for the BOT positions are every 3 years.

At integration, the Board of Proprietors invited the Board of Trustees to join the College Council to form a single governing body for the whole school.  Both governing bodies, the Proprietors who govern the non-integrated part of the school, and the Ministry of Education Board of Trustees representatives who govern the integrated school work collaboratively representing the interests of the whole College.