The purpose of this study was to examine the relationship of the Rohrer index and physical activity on motor function. The subjects were 143 elementary school children in the 5th and 6th grades. Motor function was measured based on musculoskeletal examination. The Rohrer index was calculated from height and weight, and ≥140 was defined as a tendency to be overweight. Physical activity was investigated using a self-reported questionnaire, the WHO Health Behaviour in School-aged Children in Japanese version (HBSC-J). A total of 130 students and their parents agreed to participate in this study, and the data of 127 students were analyzed. The main results were as follows: 26 students had a Rohrer index ≥140, and 60 students (47.2%) had abnormalities in one or more items of motor function. In particular, there were many who reported “Impossible to fully squat” and “Limitation of standing forward flexion”. When compared by sex, “Impossible to fully squat”, “Limitation of standing forward flexion”, and “Pain in shoulder” were particularly frequent in boys. The Rohrer index was particularly high in those who reported that it was “Impossible to fully squat”, but it was not associated with HBSC-J. “Impossible to fully squat” was particularly low in HBSC-J (days of Moderate to vigorous Physical Activity and frequency of Vigorous Physical Activity). The results suggested that children of impossible to fully squat is a lot of low activity and obesity. In conclusion, children who are unable to squat should be followed up to promote physical activity and improve obesity.