During the winter of 1861-62, Willson participated in guarding the Baltimore and Ohio Railroad and campaigns in Virginia under generals Nathaniel Banks and John Pope. He fought at the Battle of Antietam, September 17, 1862. On May 5, 1863, he was severely wounded at the Battle of Chancellorsville Virginia. He did not return to duty until September 1863 under General Joseph Hooker when the XI and XII Corps of the Army of the Potomac moved westward to reinforce the Army of the Cumberland around Chattanooga, Tennessee. There Willson participated in the battles of Wauhatchie, Lookout Mountain, Missionary Ridge, Peavine Creek, and Ringgold Gap.