Background and Aim: The imbalance between pro-oxidant and antioxidant systems often leads to further oxidative damage in the pathogenesis of both diabetes and periodontal disease. This study aimed to investigate the antioxidant and anti-inflammatory properties of melatonin in type 2 diabetes mellitus (T2DM) patients with periodontal disease (PD) under non-surgical periodontal therapy (NSPT). Materials and Methods: In this double-blind clinical trial study, 50 T2DM patients with PD were randomly allocated to intervention and control groups and received 250 mg/day (2 tablets) either melatonin or placebo 1 h before bedtime for 8 weeks. The NSPT was performed for all patients in both groups at the beginning of the study. The serum levels of interleukin-1b (IL-1b), malondialdehyde (MDA), total antioxidant capacity (TAC), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) were measured pre-and post-intervention. Results: Supplementation with melatonin in adjunct to NSPT significantly increased the serum levels of TAC, SOD, CAT, and GPx in the intervention group (P = 0.02, 0.008, 0.004 and 0.004, respectively). The mean changes of SOD, CAT, and GPx were significantly (P = 0.02, 0.04 and 0.04, respectively) greater in the intervention group compared with the control group. Also, after adjusting for confounding factors, the results did not change in terms of significance (P < 0.05). After the intervention, serum levels of MDA and IL-1b were significantly reduced in the intervention group (P < 0.001 and P = 0.008, respectively). The intervention group exhibited lower mean changes of MDA compared with the control group, and these changes were statistically significant (P = 0.008). In addition, after adjusting for confounding factors, the results did not change in terms of significance. Conclusion: The adjunctive effects of melatonin and NSPT may improve inflammatory and antioxidant parameters in T2DM patients with PD.