With the outbreak of the Civil War, he entered the army as the captain of the 2nd Iowa Infantry in May 1861. He was promoted to colonel of the 13th Iowa Infantry on December 30, 1861. Crocker fought with distinction in the Battle of Shiloh in April 1862, where he assumed command of a brigade during the first day. He commanded the "Iowa Brigade" at the Second Battle of Corinth in October, 1862. He was promoted to brigadier general on November 29, 1862.