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This paper presents an economic evaluation aimed at estimating malaria-related health care expenditures in Brazil from the perspective of the public health system. Comprehensive estimates of the costs of malaria remain scarce, in part because of limited data. Brazil has a universal health system (Sistema Único de Saúde-SUS) in which all cases of malaria are diagnosed and treated. In addition, antimalarial drugs are only available through the SUS. We compiled comprehensive data from multiple administrative sources. Expenditure indicators were calculated for municipalities and states in the Brazilian Amazon, a region where more than 99% of the country’s malaria cases are concentrated. We also developed a digital platform that allows interactive visualization of the malaria cost indicators, disaggregated by cost type and geography. Our results show that control and prevention activities are the primary cost in all states, followed by human resources and disease treatment. Expenditures per malaria notification in the Amazon ranged from PPP (purchasing power parity)-US$59.00 (2017) to PPP-US$77.00 (2016), while per capita expenditures remained relatively stable at around PPP-US$3.50. The malaria cost estimates presented here contribute to a better negotiation of the financial resources needed by the NMCP and are one of the critical pieces of information for a strategic plan of activities needed to achieve the elimination goal.