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Objectives: The aim of this study is to identify eHealth literacy level and to analyze the factors influencing eHealth literacy among middle school students in Korea. Methods: This descriptive cross-sectional study involved the administration of a self-report questionnaire. The participants were 799 middle school students. Descriptive statistics were analyzed via an independent t-test, Mann–Whitney U-test, and one-way ANOVA. Pearson correlation coefficients were used to test the correlations among variables. Multiple linear regression analysis was conducted to identify the factors influencing eHealth literacy. Results: eHealth literacy was substantially lower in students in their first year than in students in their third year of middle school. Participants with asthma, herniated disc, and atopic dermatitis had significantly lower eHealth literacy than those without the diseases. The major finding was that eHealth literacy of middle school students was influenced by their grade and number of diseases diagnosed. eHealth literacy was higher among students in their second and third years of middle school and among those who had fewer diagnosed diseases. Conclusions: eHealth literacy among adolescents is important for better health outcomes; however, middle school students with diseases had lower eHealth literacy than healthy students. Therefore, efforts to enhance eHealth literacy should focus on adolescents with diseases; moreover, health education in schools and healthcare settings for adolescents should include critical analytical skill development for better eHealth literacy.