When the Civil War broke out, Anderson joined the Confederate Army in the insurrection of his home state. He became colonel of the 11th Georgia Infantry regiment but arrived too late to participate in the First Battle of Bull Run. He saw battle during the Peninsula Campaign at Yorktown and commanded a brigade during the Seven Days Battles, Second Bull Run, Fox's Gap, Antietam, and Fredericksburg. He was promoted to brigadier general on November 1, 1862. Anderson missed Chancellorsville being with the majority of Lt. Gen. James Longstreet's First Corps operating in southeastern Virginia.