In 1861 McNeil became a colonel in the Third Missouri Infantry, but within a month he mustered out and received a commission as colonel of the Second Missouri State Militia Cavalry. He was promoted to brigadier general in November 1862. Throughout the war, McNeil never left Missouri. During the Missouri expedition of Confederate General Sterling Price, McNeil commanded Union forces during a skirmish at Marmiton River Ford. However, during the course of this campaign, McNeil's overall poor performance resulted him being relieved of his command. He commanded the district of Central Missouri for the remainder of the war and resigned in April 1865.