Stoney was born on February 26, 1888, in Camden, South Carolina, to the Reverend James Moss Stoney Jr and Jeannie Johnson Shannon. He was the third generation to become a priest, after his father and grandfather. He was educated at public schools and then moved on to study at the University of Georgia between 1904 and 1905. He left to study at the University of the South from where he graduated with a Bachelor of Arts in 1911 and a Bachelor of Divinity in 1913. While there, he was an All-Southernguard for the football team. He was later an assistant coach for The Citadel.[1] He married Mary Clifton Roberts on April 7, 1915, and together had three children. Mary died in 1924 and he then married Nora Louise Green on February 16, 1926.[2]