Background <p>Altered hip muscle activity and kinematics are key impairments in patellofemoral pain syndrome (PFPs). While neuromuscular training is beneficial, its effects on specific gluteal muscle timing and hip motion during functional tasks remain unclear. This study aimed to investigate the effects of combined balance and perturbation training on gluteal muscle activity and hip kinematics in women with patellofemoral pain syndrome.</p> Methods <p>Twenty-nine women with PFP_S were randomly allocated to an exercise group (<i>n</i> = 14) or a control group (<i>n</i> = 15). The exercise group performed 18 sessions of combined balance and perturbation training over 6 weeks. The control group received no intervention. Surface electromyography (EMG) of the gluteus maximus (GMax) and medius (GMed), 3D motion analysis of hip kinematics, pain (VAS), and function (AKPS) were assessed during a step-up task before and after the intervention.</p> Results <p>Following the intervention, the exercise group demonstrated a greater reduction in normalized gluteus maximus activity (<i>p</i> = 0.006) and a greater increase in normalized gluteus medius activity (<i>p</i> = 0.017) than the control group. Significant interactions were also found for gluteus medius activation onset (<i>p</i> &lt; 0.001) and time to peak for both gluteal muscles (GMax: <i>p</i> = 0.039; GMed: <i>p</i> = 0.023). Hip kinematics improved significantly, with interactions showing increased peak flexion (<i>p</i> &lt; 0.001) and decreased peak adduction (<i>p</i> &lt; 0.001). Clinically, significant interactions for pain (VAS, <i>p</i> &lt; 0.001) and function (AKPS, <i>p</i> &lt; 0.001) reflected greater pain reduction and functional improvement in the exercise group.</p> Conclusions <p>The 6-week combined balance and perturbation training program elicited significant between-group improvements in gluteal muscle activation patterns, hip kinematics, pain, and function in women with PFPs. These changes indicate that the intervention effectively modified underlying neuromuscular control and biomechanics, leading to symptomatic relief.</p> Trial registration <p>Clinical trial number not applicable.</p>