St. Francis of Assisi High School is run under the overall supervision of a Board of Governors comprising representatives of the following categories of stakeholders: the founders, teachers, parents, the local community, alumni, and the local government. For the proper carrying out of its functions, the Board has three committees:

• Academic, sports, games and recreation committee;
• Discipline and public relations committee;
• Finance, development, production and self help and staff and students welfare committee.