With the outbreak of the Civil War in 1861, Judah was colonel of the 4th California Volunteers at Fort Yuma, a post on the Colorado River opposite the Arizona Territory. He commanded troops at Camp McClellan near Auburn, California, until November, when he resigned his command and returned to the East. He served in the defenses of Washington, D.C. for several months. He was appointed a brigadier general of volunteers on March 22, 1862 (confirmed March 24, 1862), to rank from March 21, 1862, and served as Grant's inspector general during the Battle of Shiloh. Given field command of a division under Henry W. Halleck, Judah participated in the siege of Corinth. He received a promotion in the Regular Army in June 1862 to Major (United States) of the 4th Infantry. By autumn, he was performing administrative duties in Cincinnati, Ohio before being ordered in October to join the Army of Kentucky under Maj. Gen. Gordon Granger at Covington, Kentucky. Judah returned to a staff position during the winter of 1862–63, when he served as acting inspector general of the Army of the Ohio.