Abstract : Malaria infection is still a public health concern in Batubara District, North Sumatera, Indonesia. Spatial clusters and hotspots of malaria cases are needed to help design elimination strategies in the district. Astudy was undertaken to detect clusters and hotspot of malaria during 2018-2020 in the district. All malaria cases’ house geo-coordinate were captured by using GPS. A retrospective space-time scan statistics analysis based on population data and annual malaria incidence was performed using SaTScan. The Poisson model was employed to determine the high risk of malaria and the highest of likelihood ratio (LLR) stated as most likely cluster, with the significance level of 0.05. There were 1,229 malaria cases reported in Batubara District and the annualized average incidence was 2.73 per 1,000 population. The SaTScan analysis identified three most like clusters and three secondary clusters, while Morans’I showed that there was spatial autocorrelation of malaria in the district. The sub-district of Tanjung Tiram, Sei Suka, and Talawi were consistently the location of clusters. There is evidence for the existence of statistically significant malaria clusters in Batubara District, North Sumatera, Indonesia. These findings may assist health authorities to improve the malaria preventive strategies and develop public health interventions, with special reference to the areas where the clusters and hotspots were found to achieve the malaria elimination goal.