South Sudan hosts millions of people who were forced to flee due to conflicts and violence within the country and its neighbour, Sudan. Of those affected, more than 2 million people are internally displaced and 330,000 are refugees, mostly from Sudan.

JRS provides a variety of services in South Sudan. In Maban, JRS provides training for teachers, school materials, day care for disabled children, home visits, counselling, and emergency assistance. JRS Maban also coordinates social centres for refugee women while providing opportunities to learn tailoring, life skills, and gain psychosocial support.

JRS also provides pastoral supports to the host community, including 43 parish outstations, supporting the development of leadership groups within the parish.

In Yambio, JRS offers education scholarships to girls attending secondary school, sanitary kits to girl students, and teacher training scholarships to assist with diplomas and education degrees. JRS also provides a community and school-based peace building initiative that uses mediation and workshops for encouraging reconciliation rather than violence.