Background: There is little scientific evidence regarding the effectiveness of strengthening exercises on the foot’s intrinsic musculature in improving the lower limb on the statics and dynamics in healthy individuals. Method: To evaluate the effect on foot posture with regard to the reinforcement of the short foot exercise (SFE) compared to another without a recognized biomechanical action, which we called the “non-biomechanical function” (NBF) exercise. A randomized clinical trial was carried out with 85 asymptomatic participants with a bilateral Foot Posture Index (FPI) greater than 6 points. An experimental group (n = 42) did SFE training and a control group (n = 43) carried out NBF exercises. The foot posture was evaluated twice via the navicular drop (ND) test, and the FPI was assessed on the day of inclusion in the study (pre-intervention) and after four weeks of training (post-intervention). Results: Statistically significant values were not found in foot posture between the experimental and the control groups when comparing before and after the training. However, the foot posture was modified in both groups with respect to its initial state, and the ND value decreased. Conclusions: SFE could be considered a useful tool to deal with pathologies whose etiology includes excessive pronation of the foot.