On April 19, 1861, Negley was appointed brigadier general in the Pennsylvania Militia. He raised a brigade of Pennsylvania volunteers and served under Robert Patterson in the Shenandoah Valley in 1861. His appointment as brigadier general expired on July 20, but he was reappointed brigadier general of volunteers on October 1, 1861. In October, he was placed in command of the 7th Brigade in the Department of the Ohio. He commanded the Union expedition (raid) against Chattanooga during the Confederate Heartland Offensive. The expedition proved to be a successful demonstration of the Union Army's ability to strike deep into the heart of Confederate-held territory.[1]
On November 29, 1862, he was appointed major general of volunteers and took command of the 8th Division in the Army of the Ohio. His division became the 2nd Division in George H. Thomas' Center Wing of the XIV Corps during the Battle of Stones River. On the second day of fighting, he led a successful counterattack against Maj. Gen. John C. Breckinridge on the Union left flank. He commanded his division during the Tullahoma Campaign and the Battle of Chickamauga. During the maneuvering that preceded the Battle of Chickamauga, Negley's division, in the advance of Maj. Gen. George H. Thomas's corps, was almost trapped in a cul-de-sac named McLemore's Cove, but command confusion in the Confederate Army of Tennessee allowed them to escape in what became known as the Battle of Davis' Crossroads.[2] After the Union defeat at Chickamauga, Negley, whose division became scattered during the second day's fighting, was relieved of command, but was acquitted of any wrongdoing during the battle. The most recent study of his actions is highly critical to the general for vanishing from sight without anyone knowing where to find him.[3] Negley, however, blamed his misfortunes on the prejudices toward him of West Point graduates. When Ulysses S. Grant became general-in-chief in 1864 he discussed restoring Negley to command.[4] However, after serving on several administrative boards, Negley resigned in January 1865.
Fort Negley, built in Nashville, Tennessee in 1862 was named after him. It was the largest stone inland fort built during the war.