One of McAfee's service files includes a letter he wrote on March 5, 1862. Addressed to the Secretary of War, he introduces himself as a Jesse R. McAfee, M.D., educated at Georgia Medical College, with professional references to three physicians from Georgia then in Confederate medical service. He asks to be assigned to Glenn's Battalion, then being recruited and organized. Evidently McAfee enlisted prior to receiving word of his appointment, made effective from April 1, 1862.

McAfee corrected and returned a medical report to the War Department in Richmond VA dated May 14, 1863. The military situation in Mississippi at that time suggests that McAfee wrote from some point not yet cut off by Grant's expeditionary force. That and the absence of a parole tells us that he was not with his regiment during the siege of Vicksburg.