Throughout the autumn of 1862 the Confederate Army continued to make progress in Kentucky. However, in September, General E. Kirby Smith was halted by Union troops led by General Don Carlos Buell. in Covington. The following month General Braxton Bragg installed a Confederate government in Frankfort, Kentucky. However, this was short-lived and Bragg came under attack at Perryville (Chaplin Hills).

During the battle Don Carlos Buell lost 4,211 men (845 killed, 2,851 wounded, and 515 missing) whereas Braxton Bragg lost 3,396 (510 killed, 2635 wounded and 251 missing). After the battle Bragg was forced to retreat back to Tennessee.