In 1861, at the outbreak of the American Civil War, Twitchell enlisted in Company I, 4th Vermont Infantry. After the regiment arrived in Washington, D.C. to perform guard duty and complete training in preparation for combat, Twitchell was assigned as his company clerk. He was promoted to corporal, sergeant, and first sergeant. He took part in the Siege of Yorktown in 1862, and was wounded three times at the Battle of Lee's Mill, but none seriously. He took part in additional fighting with the 4th Vermont, including the Battle of Savage's Station and the Seven Days Battles.