The COVID-19 pandemic disrupted malaria-related health care services, leading to an excess burden of malaria. However, there is a lack of research on the indirect global impact of the COVID-19 pandemic on malaria. We aimed to assess the excess burden of malaria due to the COVID-19 pandemic in malaria-endemic countries in 2020. Based on data from the World Health Organization Global Observatory, we used estimated annual percentage changes (EAPCs) from 2000 to 2019 (model A) and from 2015 to 2019 (model B) to predict the malaria burden in 2020. We calculated the ratios between reported and predicted malaria incidence (incidence rate ratio (IRR)) and mortality rates (mortality rate ratio (MRR)). In 2020, African countries suffered the most from malaria, with the largest number of malaria cases (64.7 million) and deaths (151 thousand) observed in Nigeria. Most countries showed a decrease in malaria incidence and mortality rates from 2000 to 2019, with the strongest decline in incidence rates in Bhutan (EAPC = -35.7%, 95% CI = -38.7 to -32.5%) and mortality rates Ecuador (EAPC = -40.6%, 95% confidence interval (CI) = -46.6 to -33.8%). During the COVID-19 pandemic in 2020, there was a total of 18 million excess malaria cases and 83 291 excess deaths per model A, and 7.4 million excess cases and 33 528 excess deaths per model B globally. Malaria incidence rates increased excessively in over 50% of the malaria-endemic countries, with the greatest increase in Costa Rica (IRR = 35.6) per model A and Bhutan (IRR = 15.6) per model B. Mortality rates had increased excessively in around 70% of the malaria-endemic countries, with the greatest increase in Ecuador in both model A (MRR = 580) and model B (MRR = 58). The emergence of the COVID-19 pandemic indirectly caused an increase in the prevalence of malaria and thwarted progress in malaria control. Global efforts to control the pandemic's impact should be balanced with malaria control to ensure that the goal for global malaria elimination is achieved on time.