Thomas Keith was born in St Cyrus, Kincardineshire in 1827, one of seven sons of Rev. Dr. Alexander Keith, a Church of Scotland minister, one of the 450 who broke away to form the Free Church of Scotland, an event known as the Disruption of 1843.
Thomas Keith was educated at Aberdeen Grammar School and the Royal High School, Edinburgh then studied at Marischal College, Aberdeen where he qualified MA.