Vulnerabilities of men and women to adverse health effects due to weather variability and climate change are not equal. Uganda was among the countries in the world most affected by extreme weather events during the last decade. However, there is still limited gendered empirical evidence on the links between weather variability and health and the possible pathways through which these health effects occur. Therefore, this study analyses the effect of weather variability on illness, and the extent to which water collection ‘time burden’ mediates the relationship between weather anomalies and illness among men and women of working age in Uganda. The study also quantifies the health inequalities to be eliminated if resources are equalized.