Study Design Randomized clinical trial. Objectives To compare the effects of functional stabilization training (FST) versus standard training (ST) on knee pain and function, lower limb and trunk kinematics, trunk muscle endurance, and eccentric hip and knee torques in females with patellofemoral pain (PFP). Background A combination of hip and knee strengthening exercise appears more beneficial than quadriceps strengthening alone to improve pain and function in individuals with PFP. However, evidence on the effectiveness of these exercise programs on the biomechanics of the lower extremity is limited. Methods Thirty-one females were randomized to either the FST or ST group. Patients attended a baseline assessment session followed by 8-weeks of intervention. They were then reassessed at the end of the intervention and 3 months later. Pain was assessed with a 10cm visual analogue scale and physical function by the Lower Extremity Functional Scale and the single-leg triple hop test. The 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 torque assessment. Results The patients in the FST group had less pain at the 3 months follow-up and greater global improvement and physical function at the end of the intervention when compared to those in the ST 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. Conclusion An intervention program consisting of hip muscle strengthening and lower limb and trunk movement control exercises was more beneficial to improve pain, physical function, kinematics, and muscle strength when compared to a program consisting of only quadriceps strengthening exercises. Level of Evidence Therapy, level 2b-. J Orthop Sports Phys Ther, Epub 25 February 2014. doi:10.2519/jospt.2014.4940.