South Sudan has a high burden – among the highest in sub-Saharan Africa – of neglected tropical diseases (NTDs). This adversely affects the health and social and economic well-being of people in the country. The prevention, control and eventual elimination of many NTDs depend heavily on improved access to water, sanitation and hygiene (WASH) and, once there is access, on sound sanitation and hygiene practices. This is especially the case in NTD endemic communities. The main NTDs prevalent in South Sudan include lymphatic filariasis, schistosomiasis (bilharzia), soiltransmitted helminths (STH), onchocerciasis, trachoma, leishmaniasis and Guinea-worm disease. While the Ministry of Health (MoH) of South Sudan, through its NTD programme, had prioritized NTD/WASH partnerships and collaboration to improve the national NTD response, the programme lacked resources, capacity and a technical framework to lead the development of a harmonized NTD/WASH communication strategy.