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Several studies suggest that dietary habits are associated with poor academic performance. However, few studies have evaluated these relations after adjusting for numerous confounding factors. This study evaluated the frequency of various diet items (fruit, soft drinks, fast foods, instant noodles, confections, vegetables, and milk) and the regularity of meal times (breakfast, lunch, and dinner) all at once.A total of 359,264 participants aged from 12 to 18 years old were pooled from the Korea Youth Risk Behavior Web-based Survey (KYRBWS) for the 2009 to 2013 period. Dietary habits over the last 7 days were surveyed, including the regularity of consuming breakfast, lunch and dinner and the frequency of eating fruits, soft drinks, fast foods, instant noodles, confections, vegetables, and milk. Physical activity, obesity, region of residence, subjective assessment of health, stress level, economic level, and parental education level were collected from all of the study participants. School performance was classified into 5 levels. The adjusted odds ratios (AORs) of dietary habits for school performance were analyzed using multinomial logistic regression analyses with complex sampling. Structural equation modeling was used to analyze the effects of diet factors on school performance while considering the effects of other variables on both diet factors and school performance.Frequent intakes of breakfast (AOR = 2.34, 95% confidence interval [CI] = 2.20–2.48), fruits (AOR = 1.73, 95% CI = 1.62–1.86), vegetables (AOR = 1.48, 95% CI = 1.37–1.61), and milk (AOR = 1.35, 95% CI = 1.28–1.43) were related to high levels of school performance (each with P < 0.001). In contrast, soft drinks (AOR = 0.42, 95% CI = 0.38–0.46), instant noodles (AOR = 0.62, 95% CI = 0.55–0.70), fast food (AOR = 0.83, 95% CI = 0.72–0.96), and confectionary (AOR = 0.86, 95% CI = 0.80–0.93) were negatively associated with school performance (each with P < 0.001).This study confirms previous studies of school performance and dietary habits that find a positive association with eating breakfast and consuming fruits and milk and a negative relation with soft drinks, instant noodles, fast foods, and confections.