Background: As internet use becomes more widespread, the screen time (ST) of elementary school students increases yearly. It is known that longer durations of ST can affect obesity, physical activity, dry eye disease, and learning ability. However, the effects of ST just before bedtime have not been clarified. Therefore, we examined ST duration and timing effects on elementary school children. Methods: We conducted a survey of 7,419 elementary school students in Tokyo, Japan using a questionnaire on food education. ST duration and timing (just before bedtime) served as the explanatory variables, and the relationship between obesity, physical activity, dry eyes, and learning ability was analyzed using logistic regression analysis. Gender, school year, height, and weight were considered confounding factors. First, we examined whether ST duration and timing were related to each objective variable, using a univariate model to examine all variables. Thereafter, we performed multivariate logistic regression analyses for all variables showing a significant difference in the univariate models.Results: The results showed that the relationship between the ST duration and obesity, physical activity, and learning ability was statistically significant. The relationship between ST timing and obesity, dry eyes, and learning ability was also statistically significant. Therefore, ST timing has a greater effect on dry eyes, and ST duration has a greater effect on academic performance. Conclusion: Our findings indicate that ST in school children is related to obesity, physical activity, dry eyes, and learning ability, and they suggest that not only the duration but also the timing of ST is important.