When Civil War broke out in 1861, Bragg was appointed a brigadier-general in the Confederate Army with responsibility for the Gulf Coast. In 1862 he was assigned to a command under Albert Sydney Johnston and fought at Shiloh. Bragg replaced Johnston after his death.
In June 1862, Bragg headed the Army of Tennessee, replacing P.G.T. Beauregard. The incursion into Kentucky in August met with initial success, but was turned into failure at Perryville in October. Late in the year Braggs forces fought to a draw at Murfreesboro, but retreated southward in early 1863.
In the postwar period Bragg served as a civil engineer in both Alabama and Texas. He died at Galveston, Texas, on September 27, 1876.
Braxton Bragg was one of the most controversial Confederate commanders. He displayed excellent skills in organizing and training soldiers, but was slow to capitalize on the enemy's setbacks. Bragg also was not effective in dealing with his subordinates. His relationship with Jefferson Davis kept him in command longer than the results warranted.