Aim <p>Body mass index (BMI) and physical fitness are important indicators of health in children and adolescents, yet evidence from nationally representative samples in countries with low obesity prevalence remains limited. This study examined the association between BMI and multiple components of physical fitness among Japanese students.</p> Subject and methods <p>This cross-sectional study analyzed anonymized data from the 2023 National Survey on Physical Fitness, Athletic Performance, and Exercise Habits in Japan. Participants included 896,276 primary school students aged 10&#xa0;years and 577,925 secondary school students aged 13&#xa0;years. BMI was calculated from measured height and weight and classified into underweight, normal-weight, overweight, and obese using age- and sex-specific cutoffs. Physical fitness was assessed using eight standardized tests. Differences across BMI categories were examined using one-way analysis of variance, and quadratic regression analyses were performed.</p> Results <p>Students with normal BMI demonstrated the best performance in tests requiring body weight displacement: sit-ups, side-to-side jumps, 50-m dash, and standing broad jump. Overweight and obese students showed better performance in hand grip and sit-and-reach, while performance in the 20-m shuttle run was particularly low among obese students compared with other fitness components. Significant quadratic associations between BMI and all fitness components were observed across sex and age groups. Physical fitness was generally optimal among students with normal BMI, whereas both underweight and obesity were associated with poorer performance.</p> Conclusion <p>This study highlights the importance of addressing both low and high BMI in strategies to promote physical fitness in youth.</p>