The pathogenesis of hypertension in patients with obstructive sleep apnea (OSA) is associated with endothelial dysfunction induced by chronic intermittent hypoxia (IH). Studies have shown that administration of melatonin ameliorates oxidative injury and inflammation. This study examined the effect of melatonin on the oxidative stress, endothelial dysfunction, and inflammation during the pathogenesis of hypertension in chronic IH. Adult Sprague-Dawley rats that had received a daily injection of melatonin or vehicle were exposed to IH treatment mimicking a severe OSA condition for 14–21 days. Systolic pressure was significantly higher in the vehicle-treated (144 ± 2.7 mmHg) but not in the melatonin-treated rats (123 ± 5.1 mmHg) by 21–day IH treatment when compared with the normoxic control. Levels of malondialdehyde and the expressions of NADPH oxidase, pro-inflammatory mediators (TNF-α, inducible NO synthase, COX-2), and adhesion molecules (ICAM-1, VCAM-1, and E-selectin) of the thoracic aorta were markedly increased by 14-day IH treatment preceding the hypertensive response. Also, levels of nitric oxide (NO˙), endothelial-dependent relaxation, and the expressions of endothelial NO synthase (eNOS) and antioxidant enzymes (GPx, CAT, and Cu/Zn SOD) were significantly lowered in the IH rats. Melatonin treatment significantly mitigated the increased expression of NADPH oxidase, pro-inflammatory mediators, and adhesion molecules. Moreover, melatonin prevented the endothelial dysfunction with ameliorated levels of NO˙, endothelial-dependent relaxation, and expressions of eNOS and antioxidant enzymes. These results suggest that melatonin is protective against IH-induced hypertension and endothelial dysfunction via an antioxidant and anti-inflammatory mechanism.