The Coptic Orthodox Church is led by the Pope of Alexandria and Patriarch of All Africa on the Holy Apostolic See of St. Mark (currently Pope Tawadros II, elected 2012). The Pope is elected by the Holy Synod of Coptic bishops together with lay participation, and his authority is exercised in conjunction with the Synod. The Coptic Pope of Alexandria also holds an honorary primacy within the broader Oriental Orthodox communion as the ancient Apostolic See of St. Mark, though this is a primacy of honor rather than jurisdiction.

The Coptic Church is governed synodally: the Holy Synod of bishops is the supreme authority in doctrinal and canonical matters. The church traces its episcopal succession directly to St. Mark the Evangelist, making the Alexandrian See one of the most ancient in Christendom. The role of monasteries and bishops in maintaining theological and spiritual life is highly valued, as is the ancient office of deacon and the active participation of the laity in parish life.