Evidence for the effectiveness of repellents distributed to villages through Village Health Volunteers (VHV) in protecting against episodes of malaria is required to inform the implementation of repellents as a component of malaria control and elimination programs in the Greater Mekong Subregion. A 15-month stepped-wedge cluster randomised study including 114 villages in South-east Myanmar was implemented to test the effectiveness of distribution of topical mosquito repellent (N,N-Diethyl benzamide, 12% w/w cream) on Plasmodium spp. infection. Crossed-random effects mixed modelling was undertaken to estimate the effect of repellent distribution on Plasmodium spp. infection detected in 32,194 tests. Non-final analysis showed that, conditional on the effects of time and seasonality, Plasmodium spp. infection diagnosed by rapid diagnostic test and PCR was less likely once villages transitioned into repellent distribution. There was significant heterogeneity observed in the nature of the effect of repellent distribution between villages and we observed a greater level of heterogeneity in Plasmodium spp. infection between villages than across cross-sectional testing occasions. We observed a significant decline in Plasmodium spp. infection across the study period, independent of the intervention and seasonal variations in incidence most likely due to the increased access to malaria services provided by the VHV. Malaria services, including provision of personal protection such as repellent, provided by VHV may contribute to significant reductions in malaria.