Govan and his men participated in the Battle of Shiloh in April 1862. Following Shiloh, Govan took part in Edmund Kirby Smith's Kentucky Campaign and fought at the Battle of Perryville in October. At one point during this battle Govan temporarily commanded a brigade. He then fought at the Battle of Stones River that winter and at the Battle of Chickamauga in September 1863. Govan led a brigade in the Reserve Corps of the Army of Tennessee from August to November. During the Battle of Missionary Ridge Govan played a prominent role in the Battle of Ringgold Gap, receiving high praise from his commander, Maj. Gen. Patrick Cleburne.