St. Charles Catholic School, a not-for profit independent school, has a very unique ownership structure. It is the only school in the Archdiocese that is owned by five parishes: St. Paul the Apostle, Our Lady of Perpetual Help, St. Charles, St. John XXIII, and St. Ann's. It is managed by two boards: a Corporate Board comprised of the five parish leaders and owners responsible for the Catholicity and overall mission of the school and a Management Board of Directors responsible for the general management, strategic planning and policy development.

The Management Board of Directors consists of a minimum of 11 directors: one representative from each parish, the parent advisory chairperson, the corporate board chair and four parent representatives. Additional positions are reserved for specialists as required. Together with the Principal, the Management Board of Directors participates in the decision making process of the Board.  In addition, directors take on a portfolio dependent on the current needs of the Board and school. Needs may vary over time and include, but are not limited to, fundraising, capital campaign, maintenance, finance, marketing and legal expertise/experience. The Board may be called upon to support the Principal but does not involve itself with the day-to-day administration and operation of the school.