Hill was in Iowa when the Civil War began. Hill helped raise the 35th Iowa Volunteer Infantry Regiment, of which he was appointed Colonel on September 18, 1862. For the first several months of its existence the 35th Iowa was on garrison duty in Illinois and Kentucky until being ordered to join the Army of the Tennessee besieging Vicksburg. After the siege of Vicksburg, Colonel Hill assumed command of the 3rd Brigade, 1st Division, XVI Corps (Right Wing), a position he would maintain for much of the remainder of the war. Hill was wounded at the battles of Pleasant Hill and Yellow Bayou in 1864. He returned to regimental command at the Battle of Tupelo but was back in command of the 3rd Brigade during Price's Missouri Raid.