JRS provides various services in South Sudan. In Maban, JRS provides training for teachers; school materials; a daycare for disabled children; home visits; counselling; and emergency assistance. JRS Maban also coordinates social centres for refugee women, providing them with opportunities to learn tailoring and life skills and gain psychosocial support. JRS provides rehabilitation care through physiotherapy support to children and adults with disabilities, with those in need of assistive devices supported with various movement aid materials like wheelchairs and walking crutches. The project also provides pastoral care to the displaced population and runs the local parish. The project also organizes recreational activities for the youth that aid in positive coping mechanisms and appropriate behaviour development.

In Yambio, JRS provides education scholarships to vulnerable girls and boys attending secondary school; sanitary kits to adolescent girls attending school; essential teaching and learning supplies to schools; the construction of learning spaces; the training of school governing bodies; and certified teacher training in the Certificate and Diploma program. In Mental Health and Psychosocial Support, JRS provides counselling, distribution of dignity kits to marginalized adolescents and women, cash assistance to Persons with special needs, capacity building training to local protection structures (home visitors, care givers, protection groups, etc.) establishment and operation of Women and Girls Friendly Spaces, provision of core relief items and do referrals to other agencies for specialized services.  JRS also provides a community- and school-based peacebuilding initiative that uses mediation and workshops as well as involvement of Community Peace Ambassadors and Interfaith structures for encouraging reconciliation rather than violence. Overall, JRS Yambio supports refugees, IDPs, refugee returnees and vulnerable host community in Western Equatoria State.