Carotid endarterectomy (CEA) is the treatment of choice for carotid stenosis. Some patients develop ischemia and reperfusion (I/R) injury after CEA. This study was designed to investigate the neuroprotective effects of melatonin on I/R injury in both rats and humans. To this end, 36 male rats were evaluated, and a double-blind randomized controlled trial (RCT) including 60 patients was performed. A rat model of middle cerebral artery occlusion was used to mimic cerebral I/R. After 2 hour of occlusion and 24 hour of reperfusion, blood samples and brain tissues were harvested for further assessments. Compared with the vehicle treatment, melatonin decreased the expression of nuclear factor κ light-chain-enhancer of activated B cells (NF-κB) and S100 calcium-binding protein β (S100β) (P < 0.05) and markedly increased the expression of nuclear erythroid 2-related factor 2 (Nrf2), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) (P < 0.05). The participants in the RCT took 6 mg/d melatonin orally from 3 days before surgery to 3 days after surgery. Blood samples were drawn at the following times: baseline; pre-anesthesia; carotid reconstruction completion; and 6, 24, and 72 hour after CEA. Compared with the oral placebo treatment, melatonin decreased the expression of NF-κB, tumor necrosis factor-α, interleukin-6 (IL-6), and S100β (P < 0.05) and increased the expression of Nrf2, SOD, CAT, and GPx (P < 0.05) in patients after CEA. Our findings suggested that melatonin could ameliorate brain I/R injury after CEA and that this outcome was essentially due to the antioxidant and anti-inflammatory effects of melatonin.