Background <p>While most parasitic diseases are being eradicated, clonorchiasis remains endemic and continues to pose a significant public health burden in South Korea. The prevalence has been monitored through nationwide or endemic area surveys and sentinel surveillance systems, but surveys based on stool examinations are resource-intensive and unable to determine incidence rates and trends unless conducted nationwide. Indeed, the nation-wide surveys have not been conducted since 2012 and endemic area surveys and sentinel surveillance systems also have limitations.</p> Methods <p>We estimated the number of annual nationwide clonorchiasis cases by utilizing the National Health Insurance Service drug prescription information dataset for 2002–2023 and disease-specific prescription pattern. We then assessed trends in the overall incidence rates as well as sex-, age-, and region-specific incidence rates of clonorchiasis.</p> Results <p>Our analysis estimated that the incidence rate of clonorchiasis in Korea showed a continuous decreasing trend over 20 years. Sex-, age-, and region-specific analysis showed that males, individuals aged 40 or older, and those residing in Gyeongsang and Jeolla provinces tend to have higher incidences of clonorchiasis. This trend aligns with findings from existing surveys and other available statistics.</p> Conclusions <p>Our study highlights this novel method to estimate clonorchiasis incidence trend by utilizing publicly available drug information data. This approach will provide valuable insights for a fast and cost-effective way to estimate incidence rates and investigate trends for diseases with specific treatment options.</p>