Born on 9 May 1768 at Crieff in Perthshire, was the second son of Elizabeth Ewan and her husband, John Thomson.
He was licensed to preach by the presbytery of Haddington on 6 August 1793, and frequently assisted his uncle, John Ewan, minister of Whittingham, East Lothian.
In 1842 he received the honorary degree of DD from the University of St Andrews, and in 1847 he resigned his charge and retired to Edinburgh.
In 1795 Thomson became associated with George Gleig, bishop of Brechin, as co-editor of the third edition of the Encyclopædia Britannica.
In 1796 he became tutor to the sons of John Stirling of Kippendavie, and resigned his post on the Britannica to his brother Thomas.