The medal was conceived by Mrs. Alexander S. (Mary Ann Lamar Cobb) Erwin, daughter of Confederate politician Howell Cobb, in 1898. She and Sarah E. Gabbett designed it. The first medal was issued on April 26, 1900, to Erwin's husband, Captain Alexander S. Erwin by the Athens (Georgia) Chapter.
Charles W. Crankshaw of Atlanta, Georgia, was chosen as the contractor to produce the medal. Its first manufacturer was Schwaab Stamp & Seal Co. of Milwaukee, Wisconsin. In 1904 the contract was shifted to Whitehead & Hoag of Newark, New Jersey.
Anna Davenport Raines was the Custodian of Crosses of Honor until her death in 1913. Though intended to end in 1913, after the issuance of 78,761 medals, in 1912 it was extended indefinitely. The program finally ended in 1959.
Although no Civil War veterans are still living, the last verified Confederate veteran dying in 1951, Virginia Code section 18.2-176(b) remains in effect and makes it a Class 3 misdemeanor, punishable by a fine of not more than US$500, to "wear any Southern Cross of Honor when not entitled to do so by the regulations under which such Crosses of Honor are given."
An unofficial counterpart of the Union's GAR Medal, its wearing was never authorized on U.S. military uniforms.