Baruch began his career as a surgeon in the American Civil War; serving in the Confederate States Army and reportedly entering the service "without even having lanced a boil." He initially accepted a commission as assistant surgeon of the 3rd South Carolina Battalion on April 4, 1862, and in August of that same year, he transferred to the 13th Mississippi Infantry Regiment, in the position of surgeon. During the war, Baruch gained considerable surgical experience. After the Confederate defeat at Gettysburg in July 1863, he stayed on to treat the wounded for six weeks. Afterwards, he was imprisoned at Fort McHenry in Baltimore, Maryland, and he returned to his unit in December 1863. Following a period of ill health, he returned to the 13th Mississippi Regiment 6 months later, and he served until the end of the war.