Neglected tropical diseases (NTDs) affect the poorest of the poor. NTD programmes can and should rise to the challenge of playing a part in promoting more gender equitable societies. Gender equity shapes poverty and the experience of disease in multiple ways; yet to date, there has been little attention paid to gender equity in NTD control efforts. Drawing on a synthesis of relevant literature, the tacit knowledge and experience of the authors, and discussions at a meeting on women, girls and NTDs, this analysis paper distills five key lessons from over 20 years of gender mainstreaming in health. The paper links this learning to NTDs and Mass Drug Administration (MDA). Our first lesson is that tailored gender frameworks support gender analysis within research and programming. We present a gender review framework focusing on different MDA strategies. Second, gender interplays with other axes of inequality, such as disability and geographical location; hence, intersectionality is important for inclusive and responsive NTD programmes. Third, gender, power and positionality shape who is chosen as community drug distributors (CDDs). How CDDs interact with communities and how this interface role is valued and practised needs to be better understood. Fourth, we need to unpack the gender and power dynamics at household level to assess how this impacts MDA coverage and interactions with CDDs. Finally, we need to collect and use sex disaggregated data to support the development of more equitable and sustainable NTD programmes.