Objective To study the sex-specific lower extremity biomechanics of amateur runners with patellofemoral pain (PFP). Methods Fifteen male and ten female amateur runners with PFP were identified and enrolled in PFP group, twenty-five healthy amateur runners matched with the PFP group were recruited as control group. The kinematics and kinetics, surface electromyography (EMG) data from all the subjects in the running task were collected.Two-way analysis of variance was performed to determine the influence of group and sex on lower extremity biomechanics during running. Results Compared with control group, male amateur runners with PFP showed a greater peak knee flexion angle during the landing phase of running. Compared with control group, male and female amateur runners with PFP showed a greater peak hip adduction angle during the landing phase of running, while the peak hip adduction angle of female participants was significantly greater than that of male participants. Conclusions Amateur runners with PFP showed sex-specific lower extremity biomechanics in the running task, and the clinical intervention for PFP should be sex-specific.