He was born at Brechin, in Forfarshire and was educated at the University of Glasgow, where, at the age of twenty, he acted for a short time as substitute for the professor of Greek. He lived for a while in Germany and returned in 1784. He was elected a Fellow of the Royal Society in January 1789. 
On the death of William Robertson (1721-1793), Gillies was appointed Historiographer Royal for Scotland. In his old age he retired to Clapham, where he died on 15 February 1836. He was the older brother of judge Adam Gillies, Lord Gillies.
His History of Ancient Greece, its Colonies and Conquests was published in 1786; it was translated into French and German. This work was written with a strong Whig bias, and is now entirely superseded.
Other works included:
- View of the Reign of Frederic II of Prussia, with a Parallel between that Prince and Philip II of Macedon (1789), rather a panegyric than a critical history;
- translations of Aristotle's Rhetoric (1823) and Ethics and Politics (1786-1797);
- translations of the Orations of Lysias and Isocrates (1778); and '
- History of the World from Alexander to Augustus (1807).
- This article incorporates text from a publication now in the public domain: Chisholm, Hugh, ed. (1911). Encyclopædia Britannica (11th ed.). Cambridge University Press.