Mount Allison’s governance structure includes the Board of Regents, the President, the Senate, and the Faculty Council.

The Board of Regents is responsible for the management and control of the University. The President has supervision over and direction of the academic work and general administration of the University, subject to the direction of the Board of Regents and to the powers of Senate, which include establishing admission and program requirements as well as determining whether or not students have met the necessary conditions to receive a degree. The Faculty Council acts in an advisory capacity to the Senate and the President.