Thomas Milles (1550?–1627?) was an English customs official, known for his economic writings, in which he defended the staple system.
Son of Richard Milles of Ashford, by his first wife Joan, daughter of Thomas Glover of Ashford, and sister of Robert Glover, he was born in Kent about 1550. Educated at a free school, he entered public service about 1570, and during the next sixteen years was frequently employed in France, Flanders, and Scotland. He is said to have received a 'chapeau winged' as an augmentation to his armorial bearings for his celerity on a mission to Henry IV of France.
In 1579 he was appointed bailiff of Sandwich, Kent. He was employed by Francis Walsingham as an agent between England and Scotland in 1585, and in the following year he accompanied Thomas Randolph to Edinburgh, during the negotiations on the treaty of Berwick. He then obtained the lucrative post of customer of Sandwich. This position gave him opportunities for the interception of foreign agents and correspondence, and the government employed him in unravelling the plots of the period. In 1591 he was recommended to be sent to Brittany to view and report on the forces there, and after the expedition to Cadiz (1596) he was appointed a prize commissioner at Plymouth. In 1598 he acted as secretary to Henry Brooke, 11th Baron Cobham, Lord Warden of the Cinque Ports, and in the same year (15 June) he obtained, in reversion after Sir Ralph Bourchier, the keepership of Rochester Castle. On the death of George Gilpin in 1602 he applied, without success, for the post of councillor to the council of estate in the Low Countries. He devoted the rest of his life to the defence of the staple system. On his resignation in 1623 of the post of bailiff of Sandwich, he was succeeded (10 July) by John Philipot. His will was proved in 1627.