Although previous studies have reported an association between physical activity (PA) and myopia in school-aged children, little is known about the link between myopia and children’s functional status. The purpose of this study was to investigate dynamic balance control in relation to the daily PA levels of myopic schoolchildren aged 9–11 years (n = 52) versus a non-myopic control group (n = 53). A single leg stance test performed on the instability platform of the Biodex Balance System was used to assess balance control. The overall stability index (OSI), anterior-posterior stability index (APSI) and medial-lateral stability index (MLSI) were analyzed. PA levels were calculated using the World Health Organization European Childhood Obesity Surveillance Initiative family record form. Myopes and non-myopes were separated into three subgroups based on PA level (low, moderate and high). Myopia significantly affected OSI (F = 40.46, p < 0.001), APSI (F = 33.93, p < 0.001) and MLSI (F = 49.51, p < 0.001). There were significant differences (p < 0.001) between myopic and non-myopic children with low and moderate levels of PA, whilst there were no differences between compared children with high levels of PA. High PA levels had a positive impact on balance control in myopes. Our results showed that PA levels moderate the relationship between myopia and children’s functional status.