Randomized clinical trial. To compare the effects of functional stabilization training (FST) versus standard training on knee pain and function, lower-limb and trunk kinematics, trunk muscle endurance, and eccentric hip and knee muscle strength in women with patellofemoral pain. A combination of hip- and knee-strengthening exercise may be more beneficial than quadriceps strengthening alone to improve pain and function in individuals with patellofemoral pain. However, there is limited evidence of the effectiveness of these exercise programs on the biomechanics of the lower extremity. Thirty-one women were randomized to either the FST group or standard-training group. Patients attended a baseline assessment session, followed by an 8-week intervention, and were reassessed at the end of the intervention and at 3 months after the intervention. Assessment measures were a 10-cm visual analog scale for pain, the Lower Extremity Functional Scale, and the single-leg triple-hop test. A global rating of change scale was used to measure perceived improvement. Kinematics were assessed during the single-leg squat. Outcome measures also included trunk endurance and eccentric hip and knee muscle strength assessment. The patients in the FST group had less pain at the 3-month follow-up and greater global improvement and physical function at the end of the intervention compared to those in the standard-training group. Lesser ipsilateral trunk inclination, pelvis contralateral depression, hip adduction, and knee abduction, along with greater pelvis anteversion and hip flexion movement excursions during the single-leg squat, were only observed in the FST group after the intervention. Only those in the FST group had greater eccentric hip abductor and knee flexor strength, as well as greater endurance of the anterior, posterior, and lateral trunk muscles, after training. An intervention program consisting of hip muscle strengthening and lower-limb and trunk movement control exercises was more beneficial in improving pain, physical function, kinematics, and muscle strength compared to a program of quadriceps-strengthening exercises alone.