Charlton joined the Royal Navy in 1878 and served in the Anglo-Egyptian War in 1882. Promoted to Captain in 1903, he was made Captain (Destroyers) in the Home Fleet in 1904. He went on to be Assistant Director of Torpedos from 1911. He served in World War I as Admiral Commanding East Coast Minesweepers from 1914 and then as Commander-in-Chief, Cape of Good Hope Station from 1916. After the War he became Flag Officer commanding the East Coast of England. He retired in 1924.
He lived at Eastern House in Alverstoke in Hampshire.
In 1903 he married Laura Mary Strutt; they had three daughters. In 1910 he married Winifred Mary Stapleton-Bretherton; they had two sons and three daughters.