At the outbreak of the Civil War, Thompson was elected captain of a company in the 5th Division of the Missouri State Guard. Serving in the major battles of Price's 1861 Missouri campaign he was elected major then colonel in November 1861. In August 1862 he was recruiting a new regiment in Missouri and suffered a wound to the foot or leg at the
First Battle of Independence. Thompson was appointed Colonel of the 6th Missouri Cavalry (Confederate) November 9, 1862, as a result of
John T. Coffee's removal from command on charges of drunkenness. The regiment participated in three large Missouri raids in 1863, including the
Battle of Hartville and the defense of Little Rock, Arkansas. At the
Battle of Hartville, he was reported as doing his duty "well and nobly" while commanding his regiment. After the Battle of Hartville, he was mistakenly reported dead in enemy communications by Union Brigadier General
Fitz Henry Warren. After his many exploits during these campaigns, a command reorganization in December 1863 resulted in his replacement by another commander. ==Post-war==