Christianity entered Africa in the first century by the teachings of Saint Mark. It was primarily spread by the large Jewish population of Alexandria and become the major religion in Egypt rather quickly. The Egyptians were open to a new religion at this time because of the Roman overthrow of the Pharaoh. Previous Egyptian religious beliefs had stated that the Pharaoh was divine. With no Pharaoh, the people now sought some other definition of divinity.

Alexandria would quickly become the third center of Christianity, along with Rome and Antioch (in present day Turkey). Many of the church's early teachers were taught in the Didascalia of Athens, and would later teach there themselves. By 190 AD, the Catechal School was established in Alexandria, becoming the most important of the new Christian schools.

The legalization of Christianity in the Roman Empire would bring an end to persecution of Christians in Egypt, which led to a great rise in the popularity of Christianity. Many of the more devout Christians decided to eschew the common church and retreated into the desert to become hermits. At the same time though, Egypt was a major player in the shaping of the new, legal church under Constantine. The Bishop of Alexandria played a major role in convincing Constantine and the Council of Nicea that Arianism was heresy and vastly dangerous and helped to led to the affirmation of the principle of the Trinity. Saint Athanasius, Pope of Alexandria, created the Nicene Creed during his term, an affirmation of faith, which is still used in most Christian churches to this day. The Copts also played the major role in protecting the young religion from the Gnostics heresies.

The church in Alexandria during this time was actually the center of the new Christian religion. All three of first three great councils to define religion were heavily influenced by the Bishop of Alexandria. Indeed, the power of the Coptic Church was so great that it was commonly referred to as the "Pharaoh of the Christian Church".

The Ecumenical Council of Chalcedon condemned the Alexandrian church for its belief of monophysitism, leading the way to splitting of the Roman Catholic and Greek Orthodox churches from the Coptic Church. This problem eventually becomes more difficult as time passed. Though the Coptic Church in Egypt declined as Christianity became less and less popular to the average Egyptian, it eventually stabilized at about 10% percent of the population.