Background: Altered movement patterns of the trunk and lower limbs have been associated with patellofemoral pain (PFP). It has been assumed that increasing the strength of the hip and trunk muscles would improve lower limb and trunk kinematics in these patients. However, evidence in support of that assumption is limited. Purpose: To determine whether increases in the strength of hip muscles and endurance of trunk muscles in response to functional stabilization training will mediate changes in frontal plane lower limb kinematics in patients with PFP. Study Design: Controlled laboratory study. Methods: Thirty-one female athletes were randomized to either a functional stabilization training group that emphasized strengthening of the trunk and hip muscles or a standard training group that emphasized stretching and quadriceps strengthening. Patients attended a baseline assessment session, followed by 8 weeks of intervention, and were then reassessed at the end of the intervention period. The potential mediators that were evaluated included eccentric torque of hip muscles and endurance of the trunk muscles. The outcome variables were the lower limb and trunk kinematics in the frontal plane assessed during a single-legged squat task. Results: The eccentric strength of the gluteus muscles showed a mediation effect ranging from 18% to 32% on changes to frontal plane kinematics (decreased ipsilateral trunk inclination, pelvis contralateral depression, and hip adduction excursions) observed in the functional stabilization training group after intervention. Conclusion: Although the mediation effects were small, the results suggest that improvements in the strength of the gluteus muscles can influence the frontal plane movement patterns of the lower limb and trunk in women with PFP. Clinical Relevance: Patients with PFP might benefit from strengthening of the hip muscles to improve frontal plane lower limb and trunk kinematics during functional tasks.