According to the latest World Health Organization malaria report, 95% of 241 million global malaria cases and 96% of 627,000 malaria deaths that were recorded in 2020 occurred in Africa. Compared to 2019, 14 million more cases and 69,000 more malaria deaths were recorded, mainly because of disruptions to medical services during the COVID-19 pandemic. The aim of this study was to assess the prevalence of asymptomatic malaria cases in children and adults living in the Dzanga Sangha region in the Central African Republic (CAR) during the COVID-19 pandemic. Rapid immunochromatographic assays for the qualitative detection of Plasmodium species (P. falciparum, P. vivax, P. ovale/P. malariae) circulating in whole blood samples were used. A screening was performed in the group of 515 patients, 162 seemingly healthy children (aged 1–15) and 353 adults, all inhabiting the villages in the Dzanga Sangha region (southwest CAR) between August and September 2021. As much as 51.2% of asymptomatic children and 12.2% of adults had a positive result in malaria rapid diagnostic tests (mRDTs). Our findings demonstrated a very high prevalence of asymptomatic malaria infections in the child population. Limited access to diagnostics, treatment and prevention of malaria during the global COVID-19 pandemic and less medical assistance from developed countries may be one of the factors contributing to the increase in the prevalence of disease in Africa.