Data on the effect of increased or decreased physical activity on children’s psychological status are scarce, and effect sizes are small. This study conducted two-year longitudinal research to identify associations between physical activity, sedentary behavior, and psychological well-being in Japanese school children through a mail survey completed by 292 children aged 6–12 years. Data on sociodemographics, physical activity, sedentary behavior on weekdays and the weekend, and psychometrics (self-efficacy, anxiety, and behavioral/emotional problems) were collected using a self-reported questionnaire. A logistic regression analysis was performed, calculating odds ratios for physical activity, psychometrics, and baseline age and physical activity and sedentary behavior changes. For boys, a negative association was found between increased physical activity outside school and maintained or improved self-efficacy as opposed to a positive association in girls. Increased sedentary behavior on weekdays and long periods of sedentary behavior on weekends were associated with maintained or improved behavioral/emotional problems in girls only. This two-year longitudinal study is the first of its kind conducted in Japan. Although effect sizes were small, these results may nevertheless assist in intervention development to promote psychological well-being.
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