Background: Periodontitis is a chronic inflammatory disease that causes tissue destruction due to the imbalance in the oxidant-antioxidant system. Melatonin has anti-inflammatory, antioxidant, and immune-modulatory properties and is considered to be a biomarker and diagnostic/therapeutic agent in the pathogenesis of periodontitis. Objectives: The present study aimed to evaluate the salivary melatonin level and its changes following non-surgical periodontal therapy in patients with periodontitis. Methods: In total, 90 salivary samples were collected from 60 patients, including 30 from patients with moderate chronic periodontitis (before periodontal treatment), and 30 from the same patients one month after the non-surgical periodontal therapy, and 30 from periodontally healthy subjects (control). Salivary melatonin levels were measured using the competitive immunoassay of the human melatonin ELISA kit. Results: The highest melatonin concentration was observed in the control group (79.55 ± 59.22; P < 0.05), while the lowest concentration was observed in the pre-treatment group (P < 0.05). In addition, salivary melatonin concentration in the post-treatment group (56.58 ± 46.48) was significantly higher compared to the pre-treatment group (17.25 ± 5.79; P < 0.05). Conclusions: According to the results, salivary melatonin levels improved after non-surgical periodontal therapy, which suggests the involvement of melatonin in the pathogenesis of periodontitis. However, the exact role of melatonin requires further investigation.