Background: determining the appropriate rehabilitation protocol is essential to influence the correction of flat feet, e.g., by activating the intrinsic muscles of the foot. Therefore, this study aimed to determine the impact of the exercises activating the intrinsic foot muscles for postural control in children with flat feet, with normal and excessive body weight. Methods: Fifty-four children aged 7 to 12 were enrolled in the research. Forty-five children were qualified for the final evaluation. Each child in the experimental group was demonstrated an appropriate technique for performing a short foot exercise without compensation by extrinsic muscle. The participants then performed a supervised short foot training session once a week and on other days of the week under the supervision of caregivers for 6 weeks. Flat feet were scored on the foot posture index scale. A postural test was evaluated with a Biodex balance system SD. Statistical significance in the foot posture index scale and postural test were evaluated using an analysis of variance (ANOVA) with Tukey’s post-hoc test. Results: according to the six indices of the foot posture index scale, five indicators showed statistically significant improvement after rehabilitation. At the 8–12 platform mobility level, it was revealed that the excessive body weight group had significant improvements in the overall stability index and medio-lateral stability index, with eyes closed. Conclusion: our results indicate that a 6-week rehabilitation program based on the activation of the intrinsic muscles of the foot resulted in an improvement in the foot position. This, in turn, affected balance control, especially in children with excess body weight in conditions of closed eyes.