Viewed as a traitor in the North, Breckinridge travelled to Virginia and offered his services to the Confederacy. Commissioned a brigadier general in November 1861, he was placed in command of the so-called “Orphan Brigade,” a Kentucky unit whose troops felt abandoned by their home state. Breckinridge commanded the Reserve Corps at the Battle of Shiloh in April 1862, and his unit incurred nearly 50 percent casualties during heavy fighting at an area known as the “Hornet’s Nest.” He earned a promotion to major general shortly thereafter.
After making a failed attempt to wrest the city of Baton Rouge, Louisiana, from Union control in August 1862, Breckinridge joined Braxton Bragg’s forces near Murfreesboro, Tennessee. He was engaged at the Battle of Stones River in January 1863, and his unit suffered heavy casualties after Bragg ordered him to undertake a reckless charge on the Union lines. Breckinridge and Bragg experienced a falling-out in the wake of the battle and remained on poor terms for the rest of their tenure together.
After participating in the defense of Vicksburg in June 1863, Breckinridge served at the Confederate victory at the Battle of Chickamauga in September. During the battle his unit spearheaded attacks on the Union left flank and sustained roughly 30 percent casualties. Breckinridge next participated in Bragg’s siege at Chattanooga in the fall of 1863. During the Battle of Chattanooga in November, his unit was routed by Union General George H. Thomas’s attack on Missionary Ridge. Bragg would later blame Breckinridge for the loss at Chattanooga and even accused him of being drunk during the battle.
Despite Bragg’s accusations, in February 1864 Breckinridge was called to Richmond and charged with heading the Western Department of Virginia, a massive command that included the Shenandoah Valley. He achieved an unlikely victory at the Battle of New Market in May 1864, when cadets from the Virginia Military Institute fought alongside Breckinridge’s men and drove the superior force of Union General Franz Sigel from the Valley. Breckinridge next reinforced the Army of Northern Virginia for the Battle of Cold Harbor, in which his men repulsed a heavy assault by Union troops.
Breckinridge later joined General Jubal Early for his famous raid on Washington and was engaged at the Battles of Monocacy and Second Kernstown in July. He was then placed in command of troops in southwestern Virginia. After forces in his department won a small battle near Saltville, Virginia, in October 1864, some of Breckinridge’s troops murdered roughly 150 black troops during the Union retreat. Breckinridge was enraged by this misconduct but would have little success in his attempts to arrest the officers responsible. In November 1864 he undertook an expedition into Tennessee and won a victory at the Battle of Bull’s Gap. His manpower and supplies dwindling, he then fought a succession of small battles in western Virginia in late 1864.
In January 1865 Breckinridge was appointed the fifth and final Confederate secretary of war. He performed well in managing the fading war effort prior to the Confederate surrender in April 1865. During this time Breckinridge argued for an organized end to the hostilities and counseled Confederate President Jefferson Davis against extending the war through guerilla actions.