Thomas was born sometime in 1824 in Salem, Massachusetts, where he also joined the US Navy. He first served as a Petty Officer on the USS Congress during the Uruguayan Civil War and took part of the capture of the Argentinian blockade. During the American Civil War, Thomas was a Yeoman on the USS Richmond where his actions during the Battles of the Head of Passes, Forts Jackson and St Philip, and Mobile Bay that would earn him the Medal of Honor. The citation reads:

On board the U.S.S. Richmond, Mobile Bay, 5 August 1864; commended for coolness and energy in supplying the rifle ammunition, which was under his sole charge, in the action in Mobile Bay on the morning of 5 August 1864. He was a petty officer on board the U.S. Frigate Congress in 1842-46; was present and assisted in capturing the whole of the Buenos Ayrean fleet by that vessel off Montevideo; joined the Richmond in September 1860; was in the action with Fort McRea, the Head of the Passes of the Mississippi, Forts Jackson and St. Philip, the Chalmettes, the rebel ironclads and gunboats below New Orleans, Vicksburg, Port Hudson, and at the surrender of New Orleans.

Thomas E Atkinson received his Medal of Honor on the 31st of December, 1864 and he died a little over a year later on the 9th of March, 1868. He is buried in the Isle San Lorenzo in Callao, Peru.