Effective from May 2014, community-based traditional birth attendants (TBAs) in Yirol West County, South Sudan, were directed to start referring all women in labour to health facilities for childbirth instead of assisting them in the villages. This study aimed to understand the degree of integration of TBAs in the health system, to reveal the factors influencing the integration, and to explore the perceived solutions to the challenges faced by TBAs. A qualitative study utilising 11 focus group discussions with TBAs, 6 focus group discussions with women, and 18 key informant interviews with members of village health committees, staff of health facilities, and staff of the County Health Department was conducted. Data were analysed using qualitative content analysis. The study found that many TBAs were referring women to health facilities for delivery, but some were still attending to deliveries at home. Facilitators of the adoption of the new role by TBAs were: acceptance of the new TBAs’ role by the community, women and TBAs, perceptions about institutional childbirth and risks of home childbirth, personal commitment and motivation by some TBAs, a good working relationship between community-based TBAs and health facility staff, availability of incentives for women at health facilities, and training of TBAs. Challenges of integrating TBAs in the health system included, among others, communication problems between TBAs and health care facilities, delays in seeking care by women, insecurity, lack of materials and supplies for TBAs, health system constraints, insufficient incentives for TBAs, long distances to health facilities and transportation problems. This study has revealed encouraging developments in TBAs’ integration in the formal health system in Yirol West. However, there is need to address the challenges faced by TBAs in assuming their new role in order to sustain the integration.