In April 1861, Barnes was stationed at the Army's Fort Vancouver in Washington Territory, the second-ranking officer behind future Union general Edward Ord. On June 4, he was ordered east and departed Fort Vancouver on June 24, 1861. He soon served successively as medical director of the forces under Major General David Hunter, medical director of the Western Department, and medical director of the Department of Kansas. On May 2, 1862, he was ordered to report to the Surgeon General in Washington and upon reporting was assigned to duty as attending surgeon for the city. While on this duty he formed the acquaintance of U.S. Secretary of War Edwin M. Stanton, who quickly gained a highly favorable impression of him.