Children with behavioral problems have a high risk of impaired motor performance. However, the characteristics of balance functions and their associations with behavioral traits are unclear in this population. This study aimed to evaluate balance functions and their relationships with the degree of behavioral problems in school-aged children. A total of 209 children, aged 6–10 years, were divided into two groups, those with and those without behavioral problems, using the Strengths and Difficulties Questionnaire (SDQ). Physical assessments included the one-leg standing test (OLST), the two-step test, and the five-times-sit-to-stand test. We compared the data between groups and assessed for correlations in terms of total difficulties and the SDQ subscale scores. Children with behavioral problems showed significantly reduced the OLST results (p < 0.001) and the two-step test results (p = 0.008). The five-times-sit-to-stand test results did not show significant differences between groups. The OLST results were significantly correlated with emotional symptoms (r = −0.22, p < 0.001), hyperactivity/inattention (r = −0.29, p < 0.001), peer relationship problems (r = −0.22, p < 0.001), and total difficulties (r = −0.32, p < 0.001). Meanwhile, the two-step test results showed no significant correlation with the SDQ scores. Children with behavioral problems have poor balance function, thereby increasing the risk for instability. This suggests that the balance function of children with behavioral problems needs to be considered.