Chrysotom was born in Madytos, Eastern Thrace in 1868. His name in the world was Papadopoulos. He studied Theology at the Joachim Seminary of Constantinople, the Seminary of the Cross in Jerusalem, the Evangelical School of Smyrna and the University of Athens.
He served as a professor of Theology at the Seminary of the Cross in Jerusalem (1895), director of Rizarios School in Athens (1911) and professor of Ecclesiastical History at the University of Athens (1914 - 1923).
During his tenure, the Church of Greece changed from the Julian to the Gregorian calendar and extended its jurisdiction over the territories acquired during the Balkan Wars.