Asymmetry in the alignment of the lower limbs during weight-bearing activities is associated with patellofemoral pain syndrome (PFPS), caused by an increase in patellofemoral (PF) joint stress. High neuromuscular demands are placed on the lower limb during the propulsion phase of the single leg triple hop test (SLTHT), which may influence biomechanical behavior. The aim of the present cross-sectional study was to compare kinematic, kinetic and muscle activity in the trunk and lower limb during propulsion in the SLTHT using women with PFPS and pain free controls. The following measurements were made using 20 women with PFPS and 20 controls during propulsion in the SLTHT: kinematics of the trunk, pelvis, hip, and knee; kinetics of the hip, knee and ankle; and muscle activation of the gluteus maximus (GM), gluteus medius (GMed), biceps femoris (BF) and vastus lateralis (VL). Differences between groups were calculated using three separate sets of multivariate analysis of variance for kinematics, kinetics, and electromyographic data. Women with PFPS exhibited ipsilateral trunk lean; greater trunk flexion; greater contralateral pelvic drop; greater hip adduction and internal rotation; greater ankle pronation; greater internal hip abductor and ankle supinator moments; lower internal hip, knee and ankle extensor moments; and greater GM, GMed, BL, and VL muscle activity. The results of the present study are related to abnormal movement patterns in women with PFPS. We speculated that these findings constitute strategies to control a deficient dynamic alignment of the trunk and lower limb and to avoid PF pain. However, the greater BF and VL activity and the extensor pattern found for the hip, knee, and ankle of women with PFPS may contribute to increased PF stress.