Thomas E. Atkinson (born c. 1824, date of death unknown) was a Union Navy sailor in the American Civil War and a recipient of the U.S. military's highest decoration, the Medal of Honor, for his actions at the Battle of Mobile Bay.

He served as a petty officer on the frigate USS Congress from 1842 to 1846 and took part in the 1844 capture of the Argentinian blockade fleet outside the port city of Montevideo in the Uruguayan Civil War.

He was present at the Battle of the Head of Passes of the Mississippi River on October 12, 1861, and at an engagement against Fort McRee near Pensacola, Florida, in November 1861.

In the April 1862 Battle of Forts Jackson and St. Philip, Richmond fought Confederate ships in the Mississippi and passed artillery batteries at Chalmette, Louisiana, leading to the capture of New Orleans.

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.