At the start of the Civil War, Governor of Indiana Oliver Morton appointed Morris as the quartermaster general of the state's troops. On April 27, 1861, he was appointed brigadier general in the Indiana state militia. Soon, Morris took command of a brigade of newly raised Indiana state troops and led them into western Virginia. His troops became known as the "Indiana Brigade" and were attached to the Department of the Ohio under fellow railroader George B. McClellan. Morris was the overall Union commander at the Battle of Philippi. He fought in several other engagements in West Virginia including the battles at Rich Mountain and Corrick's Ford. Around noon on July 13, 1861, Morris attacked the rear guard of the retreating Confederate forces at Corrick's Ford on the Cheat River. Morris's men pursued the Rebels for several miles in a running skirmish before finally routing them after killing Confederate General Robert S. Garnett. The victory helped secure western Virginia for the Union. He mustered out of the militia on July 27, 1861.