Measles is a major cause of child mortality in sub-Saharan Africa. Current immunization strategies achieve low coverage in areas where transmission drivers differ substantially from those in high-income countries. A better understanding of measles transmission in areas with measles persistence will increase vaccination coverage and reduce ongoing transmission. We analysed weekly reported measles cases at the district level in Niger from 1995 to 2004 to identify underlying transmission mechanisms. We identified dominant periodicities and the associated spatial clustering patterns. We also investigated associations between reported measles cases and environmental drivers associated with human activities, particularly rainfall. The annual and 2-3-year periodicities dominated the reporting data spectrum. The annual periodicity was strong with contiguous spatial clustering, consistent with the latitudinal gradient of population density, and stable over time. The 2-3-year periodicities were weaker, unstable over time and had spatially fragmented clustering. The rainy season was associated with a lower risk of measles case reporting. The annual periodicity likely reflects seasonal agricultural labour migration, whereas the 2-3-year periodicity potentially results from multiple mechanisms such as reintroductions and vaccine coverage heterogeneity. Our findings suggest that improving vaccine coverage in seasonally mobile populations could reduce strong measles seasonality in Niger and across similar settings.