Herron mustered in as a captain in the 1st Iowa Infantry, in which he served at the Battle of Wilson's Creek. In September he was promoted to lieutenant colonel of the 9th Iowa Infantry. He was wounded and captured at the battle of Pea Ridge; thereafter, he was promoted to brigadier general. In December 1862, he marched to the battlefield at Prairie Grove in command of the Confederate forces. For this victory, he was promoted to major general. He served at the siege of Vicksburg. At the end of the war, he was appointed to negotiations with the Indians as a commissioner.
