Phytanic acid (3,7,11,15-tetramethylhexadecanoic acid) (Phyt) is a saturated branched chain fatty acid which originates after the breakdown of chlorophyll molecule, phytol. It plays an important role in a variety of metabolic disorders with peroxisomal impairments. The aim of our investigation was to evaluate the adverse effects of Phyt on synaptic functions by using synaptosomal preparation of rat brain as an in vitro model and the possible protective role of melatonin against Phyt-induced neurotoxicity. Melatonin is an antioxidant, secreted by the pineal gland. Melatonin and its metabolites have neuroprotective effects on cellular stress, by reducing reactive oxygen species (ROS) and reactive nitrogen species (RNS). In the present investigation, synaptosomes prepared from rat brain were co-treated with melatonin (10μM) and Phyt (50μM) for 2h. Co-treatment of Phyt with melatonin significantly restored the altered levels of protein carbonyl (PC) contents and lipid peroxidation (LPO). It also replenished the Phyt-induced alterations on the levels of non-enzymatic antioxidant defence reduced glutathione (GSH), enzymatic antioxidants such as catalase (CAT) and superoxide dismutase (SOD) and synaptosomal integral enzymes such as AChE, Na⁺, K⁺-ATPase and MAO. We observed that Phyt induced oxidative stress in synaptosomes as indicated by an elevation in the generation of ROS and melatonin was able to inhibit the elevated ROS generation. Moreover, the neurotoxic effects elicited by Phyt on NO level and membrane potential were totally prevented by the treatment of melatonin. The results of our investigation emphasize the potential use of melatonin as a nutraceutical and mitigatory agent against Phyt-induced oxidative stress.