This study was designed to investigate the effect of melatonin on the expression of aortic inflammatory cytokines and its underlying mechanisms in rats. Melatonin deficiency rats (Px, N = 16) were created by pinealectomy and were fed with normal diet for 16 weeks after the surgery, and compared with sham-operated rats (Con, N = 14). Serum lipid profile, glucose metabolism parameters, serum oxidative stress and inflammatory biomarkers were evaluated. The expression of inflammatory cytokines in the aorta endothelia was analyzed. To evaluate the signal transduction pathways of melatonin on the expression of cytokines, rat aortic endothelial cell lines (RAECs) were treated with melatonin, and their protein expressions of inflammatory cytokines and phosphorylation levels of relevant signal pathways were detected. At the 16th week after surgery in Px rats, their serum triglyceride, very low density lipoprotein cholesterol, free fatty acid and glucose levels were prominently elevated (all P < 0.05); serum oxidative stress biomarker malondialdehyde, serum inflammatory biomarkers oxidized low-density lipoprotein, tumor necrosis factor-α, interleukin-6 and C reactive protein were also significantly increased. Meanwhile, the expression of inflammatory cytokines: monocyte chemotactic protein-1 (MCP-1), vascular adhesion molecule 1 (VCAM-1) and matrix metalloproteinase-9 (MMP-9) of the aorta endothelia in Px rats were significantly up-regulated (all P < 0.05). In vitro, melatonin significantly decreased the expression of MCP-1, VCAM-1 and MMP-9 proteins, along with the suppression of phosphorylation levels of nuclear factor κB (NF-κB)/P65 and p38 mitogen-activated protein kinase (P38-MAPK) in RAECs. Melatonin deficiency elevates the serum inflammatory biomarkers and increases aortic inflammatory responses. Melatonin regulates these inflammatory responses by NF-κB and P38-MAPK involved pathways.