After the bombardment of
Fort Sumter in
Charleston Harbor in April 1861, the following month Thoburn enlisted as the surgeon of the
1st Virginia Infantry, a three-months regiment under Colonel
Benjamin F. Kelley. He accompanied his regiment in the
Battle of Philippi, where his patients included a wounded Colonel Kelley. In August 1861, the regiment was mustered out of service. Most of the men reenlisted in the
reorganized 1st Virginia Infantry, a three-years regiment. With Kelley still out with his wound, Thoburn was commissioned as the colonel of the regiment. He led the command in numerous small battles and engagements in what became West Virginia and also in the Shenandoah Valley in 1862 and 1863. The following year, he assumed command of a
division in the
VIII Corps and fought in the
Valley Campaigns of 1864 in the army of
Philip Sheridan. During the
Battle of Opequon or Third Winchester, as the
XIX Corps was reorganizing its lines, Thoburn's division came up from reserve and took position at the edge of a woods. Sheridan soon arrived and directed Thoburn to move forward as soon as the other division of the Eighth Corps was ready. About 3 p.m. "a mighty battle yell," from the other side of Red Bud Run announced the arrival of those troops. The Union lines advanced, and, as one participant recalled, "For thirty minutes the battle that ensued was perfectly terrific, but then the forces in our front gave way, and in an instant we were over their works, and after them with yells and shouts of victory." ==Death and legacy==