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It is important for malaria-endemic countries to address malaria control across international borders, and in particular to prioritize appropriate rapid diagnosis, treatment and surveillance. Bhutan and India aim to achieve malaria elimination by 2023 and 2030 respectively. Malaria elimination along the Indo-Bhutan border is of common concern. We delineated malaria epidemiology along the border to provide a blueprint for focusing malaria control efforts in key foci within this region. Epidemiological data from 2015 to 2019 were analyzed, as the most drastic reductions in malaria burden across most parts of India were witnessed in this time frame. Several areas of concern include low surveillance in most border districts, favorable climatic conditions for perennial malaria transmission, and movement of potential parasite carriers because of the porous borders. India and Bhutan need to control the importation/exportation of malaria cases. We highlight the foci of concern for which implementing tailor-made malaria control strategies may benefit both countries.