He was born in Thomaston, Maine to Ebenezer Thatcher and Lucy Flucker Knox, the daughter of Major General Henry Knox. Appointed to the U.S. Military Academy at West Point in 1822, Thatcher was absent on sick leave for most of the first year and resigned in April 1823. He then received an appointment as a midshipman in the Navy
Thatcher spent most of the next four years on board the frigate in the Pacific. He became a passed midshipman on 4 March 1829, and in 1830-1831 served in the schooner and sloop of war in the West Indies.