Neglected Tropical Diseases (NTDs) are both drivers and manifestations of poverty and social inequality. Increased advocacy efforts since the mid-2000s have led to ambitious new control and elimination targets set for 2020 by the World Health Organisation. While these global aspirations represent significant policy momentum, there are multifaceted challenges in controlling infectious diseases in resource-poor local contexts that need to be acknowledged, understood and engaged. However a number of recent publications have emphasised the “neglected” status of applied social science research on NTDs. In light of the 2020 targets, this paper explores the social science/NTD literature and unpacks some of the ways in which social inquiry can help support effective and sustainable interventions. Five priority areas are discussed, including on policy processes, health systems capacity, compliance and resistance to interventions, education and behaviour change, and community participation. The paper shows that despite the multifaceted value of having anthropological and sociological perspectives integrated into NTD programmes, contemporary efforts underutilise this potential. This is reflective of the dominance of top-down information flows and technocratic approaches in global health. To counter this tendency, social research needs to be more than an afterthought; integrating social inquiry into the planning, monitoring and evaluating process will help ensure that flexibility and adaptability to local realities are built into interventions. More emphasis on social science perspectives can also help link NTD control to broader social determinants of health, especially important given the major social and economic inequalities that continue to underpin transmission in endemic countries. Electronic supplementary material The online version of this article (doi:10.1186/2049-9957-3-35) contains supplementary material, which is available to authorized users.