Thomson began his medical training as a doctor’s apprentice in 1785, before studying at the universities of Glasgow and Edinburgh. Whilst in Edinburgh, he became assistant apothecary at the Royal Infirmary (1790), and president of the Medical Society from 1791–1792. In 1792 he left his position at the infirmary due to ill health and moved to London to study at John Hunter’s school of medicine. He returned to Edinburgh in 1893 and in 1800 he was nominated as a surgeon to the Royal Infirmary of Edinburgh. In 1806 he was also appointed professor of military surgery at the University of Edinburgh. In 1808 he obtained his MD from the University and King’s College of Aberdeen. In 1815 he was instrumental in the foundation of the Edinburgh New Town Dispensary.