Today, Sigma Alpha Epsilon is governed by Fraternity Conventions, which are held biennially. At conventions, members from all over the country come together to consider modifications to the Fraternity Laws, to the Ritual and to elect national officers. Between conventions, Sigma Alpha Epsilon is governed by an all-volunteer Supreme Council, composed of the Eminent Supreme Archon (President), Eminent Supreme Deputy Archon (Vice President), Eminent Supreme Warden (Treasurer), Eminent Supreme Herald and Eminent Supreme Chronicler. An Honorary Eminent Supreme Archon is also selected by the Past ESAs (Past National Presidents). The Executive Director of Sigma Alpha Epsilon, who serves as a full-time, paid staff position, holds the title of Eminent Supreme Recorder and acts as the Chief Operating Officer of the organization. He is supported by a full-time staff based at the central headquarters, known as the Fraternity Service Center and housed in the Levere Memorial Temple, as well as in the field.
There are also two other, separate entities of Sigma Alpha Epsilon, and their operations are housed at the central headquarters as well: The Sigma Alpha Epsilon Foundation and the SAE Financial & Housing Corporation.
The Sigma Alpha Epsilon Fraternity is governed more locally through Province conventions. A province is a section of the country that is composed of chapters, colonies and alumni associations in a certain state or region. These provinces meet regularly to discuss issues concerning their individual groups. Each of the 30 provinces are led by a Province Archon, who is a regional alumni volunteer supported by a Province Council, or regional alumni board of directors.