Flexible flatfoot is common among school-age children and significantly affects walking efficiency, balance stability, and joint-movement coordination in children. The demands on the skeletal structure and muscle function are increased during running;​ however, the impact of a flexible flatfoot on children's running capabilities is unclear. In this study, we aimed to investigate the effects of flexible flatfoot on the running function of school-age children. Participants with flat feet (n = 28) and typical feet (n = 27) ran on a flat surface at their chosen maximum pace. At the same time, the kinematic and dynamic parameters of their lower limb joints were monitored. A two-sample statistical analysis assessed the differences in the lower limbs' three-dimensional kinematic and dynamic parameters during running. The findings revealed a significant reduction in running velocity, stride length, and frequency, and an increased proportion in the support phase (p < 0.05) in children with flexible flat feet. The navicular drop time decreased, whereas the dynamic navicular drop height increased (p < 0.05). A notable decrease in the maximum plantar flexion and eversion torque, power, and power absorption of the ankle joint was observed (p < 0.01). Furthermore, the maximum flexion torque of the knee and hip joints and hip joint power absorption decreased (p < 0.05). The peak ground reaction force in the anteroposterior directions was reduced (p < 0.01). These results indicate that flexible flatfoot can impair the running efficiency of school-age children and lead to diminished motor stability and reduced propulsive and braking capabilities.