Human African Trypanosomiasis (HAT), commonly known as sleeping sickness, is closer than ever to being eliminated as a public health problem. We analyse archives and in-depth interviews to explore the role the national HAT programme played in the Democratic Republic of the Congo (DRC). Our political economy lens highlights how the leadership of the programme managed to carve itself substantial autonomy, forged new international alliances, and used clinical trials and international research to not only improve treatment and diagnosis but enhance its under-resourced disease control system. We discuss the sustainability of both the vertical approach embodied in the DRC’s efficient national HAT programme and its funding model at a time when the number of HAT cases is at an all-time low and better integration within the health system is urgent. Our study provides insights for collaborations between unevenly-resourced international research efforts and national health programmes.