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Background: Health screening is a preventive and cost-effective public health strategy for early detection of diseases. However, the COVID-19 pandemic has decreased health screening participation. The aim of this study was to examine regional differences in health screening participation between before and during COVID-19 pandemic and vulnerabilities of health screening participation in the regional context. Methods: Administrative data from 229 districts consisting of 16 provinces in South Korea and health screening participation rate of each district collected in 2019 and 2020 were included in the study. Data were then analyzed via descriptive statistics and geographically weighted regression (GWR). Results: This study revealed that health screening participation rates decreased in all districts during COVID-19. Regional vulnerabilities contributing to a further reduction in health screening participation rate included COVID-19 concerns, the population of those aged 65+ years and the disabled, lower education level, lower access to healthcare, and the prevalence of chronic disease. GWR analysis showed that different vulnerable factors had different degrees of influence on differences in health screening participation rate. Conclusions: These findings could enhance our understanding of decreased health screening participation due to COVID-19 and suggest that regional vulnerabilities should be considered stringent public health strategies after COVID-19.