Army of the Mississippi
He was promoted to brigadier general of volunteers in November 1861 and served as a staff officer in the Department of the Missouri. At the Battle of Island Number Ten, Hamilton led the 2nd Division in the Army of the Mississippi. He was transferred to command the 3rd Division throughout much of the Siege of Corinth. Toward the close of that campaign Hamilton was elevated to command the Right Wing of the Army of the Mississippi, consisting of the 3rd and 4th Divisions. In September 1862, he was selected for promotion to major general but this promotion was never confirmed.