Anthony returned to America with his parents soon after Anthony Todd, postmaster of Edinburgh, had stood sponsor to him as his godson; but when peace was declared after the American War of Independence, his father, in common with many American loyalists, threw up his appointments, and settled in Edinburgh with a small pension from the government.

He was educated at the Royal High School, and was nominated, by his godfather's interest, to a clerkship in the Edinburgh post office.

He graduated doctor of medicine at the University of Edinburgh in 1799, and in November of the same year he became a member of the Royal Medical Society.

[citation needed] On 16 July 1823 he submitted a request to Robert Dundas, 2nd Viscount Melville that his elder brother William John Thomson succeeds the late Sir Henry Raeburn as the King's Limner for Scotland, (the post was later given to David Wilkie).

In 1832, on the death of John Gordon Smith, he was appointed joint professor of medical jurisprudence with Andrew Amos.