Inadequate blood perfusion and ischemia–reperfusion (I/R) injury in the surgical skin flap are believed to be the major factors that cause harmful changes within the tissue and vasculature, resulting in flap necrosis. Reactive oxygen radical species (ROS), in part, are believed to play an important role in this injury. Melatonin, in many physiological conditions, has been shown to have direct and indirect antioxidative effects and free-radical-scavenging properties. Therefore, it may have a beneficial effect on I/R-induced flap injury. In this study, the possible protective effects of melatonin were investigated in I/R injury of rat epigastric (axial pattern) flaps. Ischemia was achieved for 12 h by occlusion of inferior epigastric artery. Melatonin or vehicle was administered 1 h before flap elevation and was continued for 6 days after ischemia. I/R injury elevated malondialdehyde (MDA), an end product of lipid peroxidation, and nitric oxide (NO) levels while the glutathione (GSH) content was reduced. Myeloperoxidase (MPO) activity, which is known to be related to tissue neutrophil accumulation, was found to be statistically higher in the I/R group when compared with the sham group. Administration of melatonin significantly decreased MDA, NO and MPO levels and elevated the GSH content. Moreover, melatonin reduced the flap necrosis area, which was determined using a planimetric method. In conclusion, melatonin, a potent scavenger of free radicals, plays a major role in preventing the inferior epigastric arterial I/R-induced flap necrosis, based on planimetric flap survival and biochemical results. The beneficial effects of melatonin in I/R injury implies the involvement of free radicals in flap damage.