Physical fatigue and pronated feet constitute two risk factors for running-related lower limb injuries. Accordingly, different running shoe companies designed anti-pronation shoes with medial support to limit over pronation in runners. However, there is little evidence on the effectiveness and clinical relevance of anti-pronation shoes. This study examined lower limb kinematics and kinetics in young female runners with pronated feet during running with anti-pronation versus regular (neutral) running shoes in unfatigued and fatigued condition. Twenty-six female runners aged 24.1±5.6 years with pronated feet volunteered to participate in this study. Kinetic (3D Kistler force plate) and kinematic analyses (Vicon motion analysis system) were conducted to record participants’ ground reaction forces and joint kinematics when running with anti-pronation compared with neutral running shoes. Physical fatigue was induced through an individualized submaximal running protocol on a motorized treadmill using rate of perceived exertion and heart rate monitoring. The statistical analyses indicated significant main effects of “footwear” for peak ankle inversion, peak ankle eversion, and peak hip internal rotation angles (p<0.03; d = 0.46–0.95). Pair-wise comparisons revealed a significantly greater peak ankle inversion angle (p<0.03; d = 0.95; 2.70°) and smaller peak eversion angle (p<0.03; d = 0.46; 2.53°) when running with anti-pronation shoes compared with neutral shoes. For kinetic data, significant main effects of “footwear” were found for peak ankle dorsiflexor moment, peak knee extensor moment, peak hip flexor moment, peak hip extensor moment, peak hip abductor moment, and peak hip internal rotator moment (p<0.02; d = 1.00–1.79). For peak positive hip power in sagittal and frontal planes and peak negative hip power in horizontal plane, we observed significant main effects of “footwear” (p<0.03; d = 0.92–1.06). Pairwise comparisons revealed that peak positive hip power in sagittal plane (p<0.03; d = 0.98; 2.39 w/kg), peak positive hip power in frontal plane (p = 0.014; d = 1.06; 0.54 w/kg), and peak negative hip power in horizontal plane (p<0.03; d = 0.92; 0.43 w/kg) were greater with anti-pronation shoes. Furthermore, the statistical analyses indicated significant main effects of “Fatigue” for peak ankle inversion, peak ankle eversion, and peak knee external rotation angles. Pair-wise comparisons revealed a fatigue-induced decrease in peak ankle inversion angle (p<0.01; d = 1.23; 2.69°) and a fatigue-induced increase in peak knee external rotation angle (p<0.05; d = 0.83; 5.40°). In addition, a fatigue-related increase was found for peak ankle eversion (p<0.01; d = 1.24; 2.67°). For kinetic data, we observed a significant main effect of “Fatigue” for knee flexor moment, knee internal rotator moment, and hip extensor moment (p<0.05; d = 0.83–1.01). The statistical analyses indicated significant a main effect of “Fatigue” for peak negative ankle power in sagittal plane (p<0.01; d = 1.25). Finally, we could not detect any significant footwear by fatigue interaction effects for all measures of joint kinetics and kinematics. Running in anti-pronation compared with neutral running shoes produced lower peak moments and powers in lower limb joints and better control in rear foot eversion. Physical fatigue increased peak moments and powers in lower limb joints irrespective of the type of footwear.