Franklin College:
- Gotthilf Heinrich Ernst Muhlenberg (1787-1815)
- Operated as an academy by Board of Trustees (1816-1853)
Marshall College:
- Dr. Frederick Augustus Rauch (1836-1841)
- Rev. John Williamson Nevin (1841-1853)
Franklin and Marshall College:
- Rev. Emanuel Vogel Gerhart '38 (1854-1866)
- Dr. John Williamson Nevin (1866-1876)
- Rev. Thomas Gilmore Apple '50 (1877-1889)
- Rev. John Summers Stahr '67 (1889-1909)
- Dr. Henry Harbaugh Apple '89 (1910-1935)
- Dr. John Ahlum Schaeffer '04 (1935-1941)
- Dr. H. M.J. Klein '93 (1941) (acting president)
- Theodore August Distler (1941-1954)
- William Webster Hall (1955-1957)
- Dr. Frederick deWolf Bolman, Jr. (1957-1962)
- Anthony R. Appel '35 (1962) (resigned after one week)
- G. Wayne Glick (1962) (acting president)
- Keith Spalding (1963-1983)
- James Lawrence Powell (1983-1988)
- A. Richard Kneedler '65 (1988-2002)
- John Anderson Fry (2002-present)