Thomas J. Churchill was born near Louisville, Kentucky. He was educated at St. Mary's College and studied law at Transylvania University.
He served during the Mexican War and rose to the rank of Lieutenant in a regiment of mounted infantry. He was captured by the Mexican Army and remained a prisoner of war until near the end of the conflict.
In 1848 he moved to Little Rock, Arkansas and married the daughter of Senator Ambrose Sevier and became a planter.
At the start of the American Civil War Churchill offered his services and was elected Colonel of the First Arkansas Mounted Rifles. His first combat took place at the Battle of Wilson's Creek near Springfield, Missouri. On 4 March 1862 he was promoted to Brigadier General and soon thereafter took part in Kirby Smith's Kentucky Campaign and played an important role in the victory at Richmond, Kentucky.
In the latter part of 1862 Churchill was transferred back to Arkansas and was placed in charge of the fortifications at Arkansas Post. In January 1863 the Post was attacked and seized by an overwhelming Union force under General John McLernand.
On 17 March 1863 Churchill was promoted to Major General and was ordered to transfer to the Army of Tennessee. He remained only a short time and returned to the Trans-Mississippi District and served during the Red River campaign in command of a division of Arkansas infantry. He played a major role in the Battle of Jenkins Ferry.
After the war Churchill was Arkansas State Treasurer from 1874 to 1880 and was Governor of Arkansas from 1881 to 1883.
Churchill is buried at historic Mount Holly Cemetery in Little Rock, Arkansas.