The Arkansas State Military Board assigned Cocke's regiment the designation 39th Regiment Arkansas Infantry, but this designation was rarely, if ever, used. For a time, when the Arkansas infantry regiments in the Trans-Mississippi Department were briefly designated as "Trans-Mississippi Rifle Regiments," Cocke's regiment was referred to as the 6th Trans-Mississippi (and, therefore, sometimes erroneously called the 6th Arkansas Infantry).

There was a previous 39th Arkansas Infantry -- the regiment commanded by McNeill-Hart-Rogan -- which was redesignated as the 30th Arkansas Infantry, after Turnbull's 30th Arkansas Infantry was redesignated as the 25th Arkansas Infantry. This redesignation mess was an attempt to correct a numbering error made by the Confederate War Department.