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Background Malaria remains a serious public health threat, especially in Africa. The challenge in detecting low-density Plasmodium infections via traditional microscopy hampers effective malaria surveillance and control. To date, there are no reports on nationwide community-based molecular detection for malaria in Sierra Leone.Methods In 2022, during the COVID-19 pandemic, we conducted a nationally representative, age-stratified cross-sectional epidemiological survey in Sierra Leone during the rainy season to investigate the prevalence of Plasmodium infection. A total of 2112 individuals aged 2 years or older were recruited nationwide and all participants completed the survey and provided whole blood samples. Nucleic acids were extracted from the blood samples and tested for Plasmodium infection using quantitative PCR (qPCR), with species identification performed on 400 of these samples.Results Among all 2112 samples, the Plasmodium qPCR positivity rate was 63.0% (95% CI 61.0 to 65.1), and the regionally weighted positivity rate was 62.9% (95% CI 58.3 to 67.4) in Sierra Leone. In 400 randomly selected positive samples, 97.75% were infected with Plasmodium falciparum, and 20.5% carried multiple Plasmodium species. The positivity rate significantly decreased in individuals aged 60 years above, and the rate was higher in males. Healthcare workers had the lowest positivity rate. Rural areas had a slightly higher positivity rate than urban areas yet showed no significant difference. Based on threshold cycle values, 18.6% of positive samples showed relatively low parasitaemia. Additionally, 93.5% of infected individuals self-reported as asymptomatic.Conclusions This study highlights the importance of molecular diagnosis in malaria-endemic areas for surveillance, diagnosis and treatment. The high prevalence of malaria infection among individuals aged ≥20 years, together with the high prevalence of asymptomatic, low-density infections, indicates a sustained potential transmission reservoir. Additionally, urban and rural malaria prevalence showed no statistically significant difference, a finding that underscores the need for greater attention to urban malaria.