The university's main campus is located in the city of Juba, in Juba County, Central Equatoria State, in southern South Sudan. The city of Juba is the capital of South Sudan and is the largest city in that country. The university maintains a second campus in the city of Wau, South Sudan, Western Bahr el Ghazal State, approximately 650 kilometres (400 mi), northwest of Juba. The Faculty of Arts and Social Sciences is based in Juba, the Faculties of Agricultural and Environmental Sciences and Engineering are based in Wau.
The Catholic University of South Sudan was founded in 2008, as a private institution of higher education. The Jesuit Father Michael Schultheis served as its first vice-chancellor (2008–2013), followed by Dr Matthew Pagan.