Background: Although supervised exercise therapy (SET) is a primary treatment for peripheral artery disease (PAD), the current literature is limited regarding the mechanisms contributing to increased walking distances, including how lower extremity muscle function is altered after SET. This study aimed to investigate the effects of SET on lower extremity muscle function during walking in patients with PAD. Methods: Twelve patients with PAD participated in a 6-month SET program consisting of three weekly exercise sessions (a total of 72 sessions) and adhered to the American College of Sports Medicine’s (ACSM) recommendations. Each session started with a 5 min warm-up of mild walking and static stretching of upper and lower body muscles, followed by 50 min of intermitted exercise on a treadmill, and then finished with 5 min of cool-down activities similar to the warm-up. Each patient walked across a 10 m pathway with reflective markers on their lower limbs twice: before (baseline) and after six months of participation in SET (post-exercise). Marker coordinates and ground reaction forces were recorded and imported to OpenSim software (version 4.0) for gait simulations. Muscle force, muscle power, and metabolic rate were estimated from OpenSim and compared between the baseline and post-exercise. Results: The mean plantar flexor force was not altered after SET. However, individuals’ plantar flexor muscles demonstrated improvements in force production (lateral gastrocnemius: 75–80% of stance, Cohen’s d = 0.20–0.43; medial gastrocnemius: 65–85% of stance, Cohen’s d = 0.20–0.71; soleus: 90–95% of stance, Cohen’s d = 0.20–0.26). Furthermore, plantar flexor power increased (80–95% of stance, Cohen’s d = 0.20–0.39) and this was attributed to increased power in the lateral gastrocnemius (80–85% of stance, Cohen’s d = 0.20–0.47), medial gastrocnemius (80–90% of stance, Cohen’s d = 0.22–0.60), and soleus muscles (85–95% of stance, Cohen’s d = 0.20–0.49). Similarly, other muscle groups (knee extensors, knee flexors, hip abductors, hip adductors, hip extensors, and hip flexors) also exhibited force and power increases after SET. Additionally, force and power variances were significantly decreased in several muscle groups (plantar flexors, knee extensors, hip abductors, hip external rotators, hip extensors, and hip flexors). Total metabolic rate also increased during the stance period where muscle force and power were elevated after SET (early stance: 5–25%, Cohen’s d = 0.20–0.82; mid stance: 35–45%, Cohen’s d = 0.20–0.47; late stance: 75–80%, Cohen’s d = 0.20–0.36). Conclusions: Our results suggest that from a biomechanics perspective, muscle functions during walking are improved in patients with PAD after SET; however, the improvements were generally small and were not reflected by all muscle groups.