When the Civil War began, Harrison wanted to join the Union Army but worried he would not be able to financially support his family. In 1862, Harrison visited Governor Oliver Morton, who was worried about the state’s lack of soldiers. The governor asked Harrison to recruit a regiment, but not serve. Once Harrison had assembled his soldiers, Morton offered him command of the unit, but he refused because of his lack of military experience. Harrison was then commissioned a second lieutenant. He spent most of his first two years doing reconnaissance and guarding railroads in Kentucky and Tennessee. By 1864, Harrison was moved to the front lines and led a brigade at the Battles of Resaca, Cassville, New Hope Church, Lost Mountain, Kennesaw Mountain, Marietta, Peachtree Creek, and Atlanta.