In 1861, Brown was commissioned as lieutenant colonel of the 7th Missouri Infantry. In May 1862 he resigned this commission to become a brigadier general in the Missouri state militia. In January 1863 he commanded the defenses at Springfield, Missouri, where he was injured and lost the use of one arm. In 1864 he resisted guerilla raids and skirmishes in the District of Central Missouri. At the Battle of Westport, Missouri, he was relieved of command and arrested for failure to obey an order to attack. In January 1865, he took command of the District of Rolla, his last assignment of the war.
