Studies have shown the potential effects of sedentary behavior and physical activity on not only physical and mental health but also academic performance in children. Nevertheless, studies have only focused on either sedentary behavior or physical activity. Examining the joint effects of both behaviors on academic performance provides detailed insights into the patterns of these behaviors in relation to children's academic achievement. The present study investigated the joint longitudinal associations of physical activity and screen time with academic performance among Japanese children. The screen time and physical activity of 261 children aged 7-10 years were assessed, and their academic performance was evaluated one year later. Multivariate logistic regression analysis was used to examine the joint associations of screen time and physical activity with academic performance adjusted for demographic characteristics. Children with low screen time and physical activity had 2.04 (95% confidence interval: 1.11-3.78) times greater odds of having high academic performance compared to children with high screen time and low physical activity, while children with low screen time and high physical activity had 2.75 (1.17-6.43) times greater odds (boys; 4.12 (1.19-14.24)). Low screen time was related to high academic performance after one year, regardless of the physical activity level.