At the outbreak of the Civil War in 1861, Blunt was appointed lieutenant colonel of the 3rd Regiment Kansas Volunteer Infantry, a part of James Lane's Kansas Brigade, an irregular partisan force not accepted into the Union Army until reorganized in April 1862. In April 1862, Blunt was appointed brigadier general of volunteers and given command of the Department and Army of Kansas. He ordered Colonel William Weer to lead the "Indian Expedition" in 1861 which succeeded in occupying Fort Gibson and arming three regiments of Native Americans. Blunt's forces were defeated in the First Battle of Newtonia, and the Army of Kansas was incorporated into the Army of the Frontier as the 1st Division. Blunt led his division of Cherokee and Kansas volunteers to victory at the Battle of Old Fort Wayne. In December 1862, Blunt's division was joined by the 2nd Division under Francis J. Herron. The combined forces met Confederates under Thomas C. Hindman at the Battle of Prairie Grove. While tactically a draw, the battle was a strategic victory for the Union.