Background: The prevalence of malaria infection in time and space provides important information on the likely sub-national epidemiology of malaria burdens and how this has changed following intervention. Model-based geostatitics (MBG) allow national malaria control programmes to leverage multiple data sources to provide predictions of malaria prevalance by district over time. These methods are used to explore the possible changes in malaria prevalance in Malawi from 2010 to 2017. Methods: Plasmodium falciparum parasite prevalence (PfPR) surveys undertaken in Malawi between 2000 and 2017 were assembled. A spatio-temporal geostatistical model was fitted to predict annual malaria risk for children aged 2–10 years (PfPR2–10) at 1×1 km spatial resolutions. Parameter estimation was carried out using the Monte Carlo maximum likelihood methods. Population-adjusted prevalence and populations at risk by district were calculated for 2010 and 2017 to inform malaria control program priority setting. Results: 2,237 surveys at 1,834 communities undertaken between 2000 and 2017 were identified, geo-coded and used within the MBG framework to predict district malaria prevalence properties for 2010 and 2017. Nationally, there was a 47.2% reduction in the mean modelled PfPR2-10 from 29.4% (95% confidence interval (CI) 26.6 to 32.3%) in 2010 to 15.2% (95% CI 13.3 to 18.0%) in 2017. Declining prevalence was not equal across the country, 25 of 27 districts showed a substantial decline ranging from a 3.3% reduction to 79% reduction. By 2017, 16% of Malawi’s population still lived in areas that support PfPR2-10 ≥ 25%. Conclusions: Malawi has made substantial progress in reducing the prevalence of malaria over the last seven years. However, Malawi remains in meso-endemic malaria transmission risk. To sustain the gains made and continue reducing the transmission further, universal control interventions need to be maintained at a national level. © 2019 Chipeta MG et al.