Patellofemoral pain (PFP) is often associated with impaired muscle strength, flexibility, and stability. It has been suggested that inter-leg asymmetries have an important role in increasing the risk of musculoskeletal injuries, including PFP. Thus, the aim of this study was to identify significant asymmetries and determine the effects of a symmetry targeted exercise program in patients with PFP. Eighteen patients aged 13 to 54 years (24.17 ± 12.52 years) with PFP participated in this study. Strength, flexibility and stability outcomes of the trunk, hip, knee and ankle muscles were assessed. A single-group pretest–posttest design was used to assess changes in inter-leg and agonist–antagonist asymmetries resulting from the 8-week period of the supervised exercise program. Results indicated a significant improvement in inter-leg symmetry regarding bilateral stance in a semi-squat position (p = 0.020, d = 0.61, df = 17) and ankle plantarflexion (p = 0.003, d = 0.32, df = 17) and ankle dorsiflexion strength (p < 0.001, d = 0.46, df = 17). In addition, the ratio of ankle dorsiflexion/plantarflexion (p = 0.036, d = 1.14, df = 17) and hip extension/flexion (p = 0.031, d = 0.94, df = 16) changed significantly during the intervention period. To our knowledge, this was the first study to evaluate inter-leg asymmetries resulting from a period of a supervised exercise program. The results indicate that an exercise program focusing on individual asymmetries may influence specific deficits and contribute to better rehabilitation outcomes.