From March 28, 1862, until May 1, 1863, Yancey served in three sessions of the Confederate Congress. While there, he reluctantly supported the Confederate Conscription Act of April 16, 1862, but was instrumental in allowing many state exemptions to the draft as well as the unpopular exemption for one overseer for every twenty slaves, an exemption that applied to about 30,000 men. He unsuccessfully argued against the excessive use of secret, unrecorded sessions of Congress and generally pursued a states' rights position in regard to the exercise of national war powers in general and impressment of supplies and slaves by the federal Confederate government in particular. On military matters, Yancey wanted details provided to Congress on reports of execution without trials of Confederate soldiers by General Braxton Bragg, questioned the reasons Virginia had twenty-nine brigadier generals while Alabama only had four, authored a resolution condemning drunkenness within the army, and joined in demands that Davis account for complaints on the military administration of the Trans-Mississippi District.