Walker volunteered at the outbreak of American Civil War as a surgeon – first for the Army, but was rejected because she was a woman (despite having kept a private practice for many years). She was offered the role of a nurse but declined and chose to volunteer as a surgeon for the Union Army as a civilian. The U.S. Army had no female surgeons, and at first, she was allowed to practice only as a nurse. During this period, she served at the First Battle of Bull Run (Manassas), July 21, 1861, and at the Patent Office Hospital in Washington, D.C. She worked as an unpaid field surgeon near the Union front lines, including at the Battle of Fredericksburg and in Chattanooga after the Battle of Chickamauga. As a suffragist, she was happy to see women serving as soldiers, and alerted the press to the case of Frances Hook, in Ward 2 of the Chattanooga hospital, a woman who served in the Union forces disguised as a man. Walker was the first female surgeon of the Union army. She wore men's clothing during her work, claiming it to be easier for high demands of her work.