The COVID-19 pandemic has resulted in massive global disruptions with considerable impact on the delivery of health services and national health programmes. Since the detection of the first COVID-19 case on 5th March 2020, the Royal Government of Bhutan implemented a number of containment measures including border closure and national lockdowns. Against the backdrop of this global COVID-19 pandemic response, there was a sudden surge of locally-transmitted malaria cases between June to August 2020. There were 20 indigenous cases (zero Plasmodium falciparum and 20 Plasmodium vivax) from a total of 49 cases (seven P. falciparum and 42 P. vivax) in 2020 compared to just two from a total of 42 in 2019. Over 80% of the cases were clustered in malaria endemic district of Sarpang. This spike of malaria cases was attributed to the delay in the delivery of routine malaria preventive interventions due to the COVID-19 pandemic. As a result, Bhutan is unlikely to achieve the national goal of malaria elimination by 2020.