Christianity was first brought to this territory by the Church of Byzantium in the sixth century. The local Church later passed to the Coptic Patriarchate of Alexandria. The end of the Christian Kingdom of Nubia, in the early fourteenth century, led to the almost total disappearance of Christianity, with only a few Franciscan communities remaining in the region.
It was reintroduced in late 19th century by Italian missionary St. Daniel Comboni (1831-1881), founder of the Missionaries of the Heart of Jesus and of the Congregation of the Pious Mothers of Nigrizia, also known as the Comboni Missionary Sisters, who managed to re-establish the Church in Sudan, and in particular in South Sudan where there are still operating today.
Their intensive missionary activity allowed Christianity to expand at an increased rate between 1901 and 1964, strengthening the national identity of the people of South Sudan, as distinct from the Arab and Muslim population of the North.
Source: Vatican News