From the early Masters who administered the School, to those who have established it as one of the country’s leading educational institutions, QE’s headmasters have made the School what it is today.
| William Moffett | 1579-1591 |
| John Boyle B.D. | -1597 |
| Thomas Turner MA | 1598-1599 |
| Richard Boyle MA | 1599-1602 |
| Thomas Meriall MA | 1608-1612 |
| John Smith | 1612-1618 |
| Matthias Milward MA B.D. | -1633 |
| George Smalwood MA | 1633-1644 |
| Francis Storr BA | 1645-1646 |
| John Smith MA | 1646-1651 |
| Thomas Broughton BA | 1652-1654 |
| William Sclater MA | 1654-1663 |
| Daniel Barnes MA | 1663- |
| Thomas Gregory | c.1677 |
| Joseph Thomas MA | -1689 |
| James Barcock MA | 1689-1719 |
| Edward Saunder | 1720-1727 |
| Francis Fielding | 1727-1740 |
| John Gray | 1740-1787 |
| John Smith | 1787-1796 |
| Samuel Lambrick | 1796-1800 |
| George Porter B.D. | 1800-1801 |
| William Marr B.D. | 1801-1825 |
| William Austin Morgan | 1825-1837 |
| James Alexander Wood BA | 1837-1840 |
| Nathaniel Baily | 1840-1842 |
| Thomas Cox LL.D. | 1842-1852 |
| Clayton Palmer LL.D. | 1852-1854 |
| Charles Presdee | 1854-1873 |
| John Bond Lee MA | 1875-1906 |
| William Lattimer MA | 1906-1929 |
| Ernest Harold Jenkins MA | 1930-1961 |
| Timothy Bracey Edwards MA | 1961-1983 |
| Eamonn Harris MA | 1984-1999 |
| John Marincowitz PhD | 1999-2011 |
| Neil Enright MA MBA | 2011- |