 Clopton withdrew from the United States House of Representatives in 1861 and enlisted as a private in the Confederate Army in the Twelfth Alabama Infantry for one year.Afterwards he represented Alabama in the First Confederate Congress and the Second Confederate Congress.He was among a group who wrote to the Alabama governor petitioning for the pardon of Robert Wynn, doorkeeper of the provisional Congress, who had been convicted of assault with intent to murder but later reconciled with his victim.