The establishment of the Coptic Evangelical Church in the goes back to the beginning of the twentieth century as an offshoot of the Evangelical Church of Egypt.

After the fall of the Mahdist rule in the in 1898 and the establishment of the Anglo-Egyptian Condominium, many were enrolled in the service of the Sudan government. As there were among them about seventy Evangelicals, Jabra Hanna was delegated by the mother church of Egypt to give them pastoral care (1900).

The Evangelical Church in was officially organized in December 1907, and elders were ordained. This was, and still is, the mother of all the other Egyptian churches in the —that is, the churches of ‘Atbarah, Port Sudan, Kuraymah, Wadi Halfa, Wad Madani, al-Qadarif, and al-Ubayyid. All services in these churches are conducted in Arabic. As Southern Sudanese began migrating to the north in large numbers (as from 1960), new churches were opened in Kusti, al-Duwaym, Shandi, and Husayhisah, where services are conducted in Arabic or in tribal languages of the Southern Sudan.

In 1932, owing to financial difficulties, many left the Sudan. The churches of ‘Atbarah, Wadi Halfa, Kuraymah, and Port were closed. Later on those in ‘Atbarah and Port Sudan were reopened.

In 1946 the Synod of the Nile of the Evangelical Church of Egypt, in response to a petition from the Presbytery, gave permission for the organization of the Upper Nile Presbytery, which included the congregations of Doleib Hill and Nasir.

In March 1956 the Church of Christ in the Upper Nile was officially recognized by the Presbytery and later also by the United Church in the USA.

In March 1964 all the foreign missionaries were expelled from southern by order of the government. The local pastors (about 100) took over all the church administration in the South. The total number of Evangelicals of Coptic (Egyptian) origin is about 2,000; those of African origin (southern Sudan) is estimated at about 150,000.

In 1970 the Church of Christ in the Upper Nile merged with the Evangelical Church in the northern Sudan, under the official name of Church in the Sudan.