St. Francis Xavier Primary School is registered with ASIC as a company Limited by Guarantee. As such the school is governed by a Board of Directors.

The School Board is responsible for the management of the school within the terms established by the Governing Authority, the Institute of Sisters of Mercy and the Diocese of Ballarat. The members of St. Francis Xavier Primary School, Ballarat East Ltd are Sr Berenice Kerr RSM (representing the Institute of Sisters of Mercy Australia and Papua New Guinea) and Fr Kevin Maloney (representing the Diocese of Ballarat).

The Board meets regularly to establish and review general policy, to receive regular reports from the School Principal, to consider the financial situation and to undertake long-term planning for the School.

The predominant objectives for which the Company is established are:
(a) To provide educational services within the field of Catholic primary education in the Catholic Diocese of Ballarat
(b) To provide students with a primary education, including a curriculum for all students in religious instruction in accordance with the precepts, teachings and practices of the Catholic Church as determined from time to time by the Bishop
(c) To carry on or assist in the carrying on and promotion of the mission of the Catholic Church in conformity with canon law and in fidelity to the teachings and example of Christ, the teaching of the Catholic Church and the spirit of Catherine McAuley, the Foundress of the Sisters of Mercy.

The Directors of the Board participate in various sub-committees. The sub-committees consist of Board Directors, members of the School Leadership Team, staff, parents and representatives from the wider community.