Exercise improves physical health and positively impacts physical functions in children. Additionally, the habitual exercise established during childhood often continues into adulthood. Therefore, childhood is an important period for establishing healthy habits. Investigating the relationship between the presence or absence of daily exercise and physical functions may provide important information to confirm poor physical function in children with poor exercise habits. Therefore, this study examined the relationship between exercise habits as defined by the Japanese Ministry of Health, Labor, and Welfare and physical function in children aged 9-12 years. Approximately 239 children were included in this study. Participants answered a questionnaire about their exercise habits. We evaluated the skeletal muscle mass index, grip strength, standing broad jump, one-leg standing time, and gait deviation index. Logistic regression analyses were performed to assess exercise habit association with skeletal muscle mass index, physical function, and gait deviation index after adjusting for sex. Of the 239 children, 75.5% (n = 178) had exercise habits. A significant association was noted between exercise habits and skeletal muscle mass index and standing broad jump (skeletal muscle mass index: OR, 1.84; 95% CI, 1.01-3.36 and p<0.05; standing long jump: OR, 1.02; 95% CI, 1.00-1.04 and p<0.05). In conclusion, exercise regardless of exercise level for at least 30 min per day, 2 days per week, for at least 1 year is important for skeletal muscle mass and instantaneous lower limb muscular strength development in school-aged children.