When the Civil War broke out, he joined the Confederate Army in defense of his home state. He became Colonel of the 11th Georgia but arrived too late to participate in the First Battle of Manassas. He saw battle during the Peninsula Campaign at Yorktown and commanded a brigade during the Seven Days Battles, Second Manassas, Turner's Gap, Sharpsburg, and Fredericksburg. Anderson missed out on Chancellorsville being with the majority of Longstreet's I Corps operating in southern Virginia.
Longstreet's men rejoined the Army of Northern Virginia in time for the Gettysburg Campaign. Anderson fought around Devil's Den and the Wheatfield at Gettysburg, where he was wounded. He recuperated in the Charleston area while Longstreet's Corps went to Georgia. Anderson did not rejoin his men until the Siege of Knoxville. He saw heavy action in 1864 at the Wilderness, Spotsylvania, Cold Harbor, and the operations around Richmond and Petersburg. He surrendered with Lee at Appomattox Court House in April 1865.
After the war, Anderson became a railroad freight agent and police chief in Atlanta, Georgia. He later moved to Anniston, Alabama, becoming police chief there and county tax collector. Anderson died April 4, 1901 and is buried in Anniston's Edgemont Cemetery.