This study investigated the collapse of the medial longitudinal arch (MLA) as a risk factor for medial tibial stress syndrome (MTSS), hypothesizing that overuse of extrinsic foot muscles to prevent MLA collapse can lead to disability. Twenty healthy adults (age: 20.8 ± 0.8, height: 162.2 ± 10.4, weight: 54.9 ± 9, BMI: 20.8 ± 1.7) (39 feet) with a foot posture index score below 6 and no recent lower extremity orthopedic history participated. Ultrasonography measured foot muscle cross-sectional areas, while three-dimensional motion analysis using VICON assessed foot kinematics during gait, focusing on navicular height at initial contact (ICNH) and dynamic navicular drop (DND) during the stance phase. Hierarchical cluster analysis based on ICNH and DND compared muscle cross-sectional areas between clusters using ANOVA or Kruskal–Wallis test. The analysis indicated that ICNH was lower in clusters 1 and 3 than in cluster 2, and DND was smaller in clusters 1 and 2 than in cluster 3. Although there was no significant difference in muscle cross-sectional area between the clusters, the flexor hallucis longus tended to be thicker in cluster 1 than in cluster 3 (p = 0.051). The findings suggest that flexor digitorum longus may help prevent MLA compression during loading, indicating that overuse of extrinsic foot muscles may contribute to MTSS development.