Thymoquinone have been shown to decrease ischemia-reperfusion injury (IRI) in some tissues such as gastric mucosa and brain. In this study, the effect of thymoquinone was evaluated on an animal model of IRI in the rat hind limb. Hind limb ischemia was induced by clamping the common femoral artery and vein. After 2 h ischemia, the clamp on the femoral vessels was taken off and the animal underwent 1 h reperfusion. Muscle injuries were evaluated by recording the electromyographic (EMG) potentials and performing some biochemical analysis including thiobarbituric acid reactive substances (TBARS), total sulfhydryl (SH) groups, and antioxidant capacity of muscle using ferric reducing ability of plasma (FRAP) assay. Ischemia was induced using free-flap surgery in skeletal muscle. Thymoquinone (20, 40 and 80 mg/kg) and normal saline (10 ml/kg) were administered intraperitoneally 1 h prior to reperfusion. The average peak-to-peak amplitude during ischemic reperfusion was significantly increased in thymoquinone groups in comparison with the control group. Following thymoquinone administration, the total SH contents and antioxidant capacity were elevated in muscle flap. The malondialdehyde (MDA) level was declined significantly in test groups. It is concluded that thymoquinone have some protective effects against the muscle tissue injury caused by lower limb ischemia-reperfusion.