John Henry Holliday, the son of Henry Burroughs Holliday, and Alice Jane McKey, was born on August 14, 1851 in Griffin, Georgia. In 1862, when John Henry was thirteen, his father Major H. B. Holliday resigned from the Confederate States Army for health reasons and moved to Valdosta, away from the threat of Union forces.

John Henry Holliday entered the Pennsylvania college of Dental Surgery in 1872 and returned to Valdosta.