With the outbreak of the American Civil War, Neil enlisted in the Second Ohio Volunteer Infantry on April 17, 1861. During his three month commitment, he saw action in First Battle of Bull Run. Neil returned to Ohio at the end of his enlistment and sought a commission. After helping to recruit a volunteer regiment, Neil was made a lieutenant on October 1, 1861 and saw his regiment attached to William Tecumseh Sherman's division under General Ulysses S. Grant.