The aim was to examine the effects of muscle fatigue of knee extensor and hip abductor muscles on dynamic standing balance of patients with patellofemoral pain syndrome (PFPS) compared to their healthy matched controls. Thirty participants (15 with PFPS, 15 controls) were recruited. Isolated muscle fatigue of two muscles was induced isokinetically in three separate sessions (one practice and two testing sessions) with a rest interval of at least 72h. In each testing session, fatigue protocol of only one muscle group was performed for the both legs with a rest time of 30min. After determining peak torque, participants were encouraged to perform continuous maximal concentric-eccentric contraction of the target muscle until the torque output dropped below 50% of peak value for 3 consecutive repetitions. Immediately after the completion of the fatigue protocol, balance testing of participants was undertaken during single leg standing using the Biodex stability system. Balance stability measures included the overall, anteroposterior and mediolateral stability indices (OSI, APSI and MLSI, respectively). Patients exhibited decreased balance stability in the sagittal plane (higher APSI) when compared to controls. Isolated muscle fatigue of the knee extensors and hip abductors reduced balance stability in both study groups. Fatigue of hip abductors was associated with greater balance instability (higher OSI and APSI) than fatigue of knee extensors.