The Third Military District existed in the American South during the Reconstruction era that followed the American Civil War. It comprised Georgia, Florida and Alabama and was headquartered in Atlanta.

Originally commanded by General John Pope, after his removal by President Andrew Johnson on December 28, 1867, General George Gordon Meade took his place.He served at the current location of Fort McPherson until August 1868 after Alabama and Florida had been were re-admitted into the United States.

Because of the expulsion of Blacks from the Georgia legislature, a new military leader was appointed on December 22, 1869, General Alfred Terry. In January, he returned the legislators and ousted 29 Democrats. In February, the Fifteenth amendment was ratified by Georgia and by July it was re-admitted into the Union.