For most of its history, academic structure the University of Edinburgh was managed by Faculties. From 2002, the structure of the university changed, with 3 new Colleges each overseeing various Schools.

The regenting system operated from the opening of the university in 1583. Each 'regent' took the same class through all four years of their degree course, teaching all subjects himself, then recommenced the cycle with a new first-year (or ‘Bajan’) class. In an effort to remodel Edinburgh University along European lines, William Carstares persuaded the Town Council of Edinburgh (16 June 1708) to abolish regenting in favour of a professorial system that assigned each of the subjects on the Master of Arts curriculum to a single teacher. The newly created chairs were offered to the existing regents. Thus Laurence Dundas (1662-1734) became Professor of Humanity, William Scott "primus" (1672-1735), Professor of Greek, Colin Drummond (c1685-1753), Professor of Logic and Metaphysics, Robert Stewart (1675–1758), Professor of Natural Philosophy, and William Law (d. 1729), Professor of Moral Philosophy.

The foundation of the Faculty of Divinity coincided with the foundation of that Chair in 1620, following the separation of the roles of Principal and Professor of Theology. While the first medical degree was conferred in 1705, the foundation of a dedicated Faculty had to wait until 1726. Similarly, the creation of a Regius Professorship of Public Law in 1707 preceded the establishment of that Faculty and the end of the Regenting system in 1708 was the precursor to establishing the Faculty of Arts.

An Ordinance of 1893 reconstituted the University into six Faculties, each with its own Dean: Arts, Divinity, Law, Medicine, Music and Science. Deans were elected by their respective Faculties. The Royal (Dick) Veterinary College was reconstituted as an integral part of the University of Edinburgh in 1951 and became a full faculty in 1964.