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Leaving his medical practise and a store in Missouri, Dr. Hunter volunteered to serve the South at the outbreak of the Civil War. Each regiment for the South was assigned a surgeon and an assistant surgeon. Before the war, the medical corps for the Union Army had one Surgeon General, thirty surgeons and eighty-three assistant surgeons. Twenty-four of these doctors were resigned to go south and three were dropped for disloyalty. By the end of the war, the medical corps for the North numbered 11,000. The Surgeon General for the South was Dr. Moore. Moore wanted better quality surgeons so, to hold a Confederate commission, doctors had to pass an exam and boards. Moore's dislike of filthy camps and hospitals led to "pavilion" hospitals with ample ventilation and bed space for 80 - 100 patients. He foresaw drug, hospital surgical supplies, and instruments shortages. He established labs and purchased what he could from Europe. He also distributed a book on native herbs and plants of the south believed to have curative qualities.

After passing his medical board exam, Dr. A. J. Hunter was assigned to the 6th Louisiana Infantry, also called as Lee's Tigers, known for wearing Irish Tartan sashes. After his assignment, Hunter was sent to Orange Court House General Hospital in Virginia. General hospitals were often a stepping stone between the battlefield care and permanent hospitals. During the fall and winter, Dr. Hunter spent his time at the general hospital and, with the coming of the spring and summer campaigns, he was assigned where he was needed. After the 6th Louisiana Infantry was almost wiped out, Hunter was assigned to the 3rd South Carolina Regiment and, in 1863, he was attached to Jeb Stuart's Horse Artillery Cavalry.

With the retreat of the battle of Gettysburg, Dr. Hunter (along with 70 other medical personnel) were captured near Winchester, Virginia. They were incarcerated at Fort McHenry (nicknamed the "Baltimore Bastille"), whose population of POW’s grew rapidly from 126 to 6,957. Prisoners at Fort McHenry were given a blanket but were denied bedding, chairs, stools, wash basins and eating utensils. Improvised eating utensils were fashioned from whittled wood with "hard tack" for a plate. Breakfast generally consisted of coffee and hard tack; lunch was bean soup and hard tack; dinner was either half a pound of salt pork or pickled beef, coffee and hard tack. Hard tack was a hard flour biscuit (called "Johnny Cake" in the South) and it was often moldy and contained wriggling weevils. As well, the meat served to Dr. Hunter and the other POW's was often rancid.

Dr. Hunter remained in detention at Fort Mc Henry until November 1863 when he was paroled/exchanged. After agreeing not to bear arms against the North, A. J. Hunter headed home to Missouri. In his absence, some key things had happened in Missouri. First, his daughter, Lizzie Kate Longstreet Hunter, was born on January 25, 1863. Secondly, Missouri passed a state law in January of 1864 declaring that anyone suspected of holding southern sympathies could be hanged, shot or imprisoned, and their goods could be sold or destroyed. The Hunter family holdings had been burned and most of their things were destroyed. For a short time, Susannah and the children were jailed by Northern forces. Once, while trying to hush young Davis in jail, a guard told Susannah Hunter to silence her southern brat. This caused Susannah Hunter to vow to include the names of Southern generals in all her future children's names, hence the name "Lizzie Kate LONGSTREET Hunter."

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