Syzygium cumini (L.) Skeels (Sc) belongs to the medicinal plants with an important source of phenolic compounds. Sc has been shown to possess antioxidant and anti-inflammatory properties. Methylmercury (MeHg), a highly toxic environmental pollutant, induces oxidative stress and dysfunction in many cell types. This study was aimed to evaluate the effect of aqueous seed extract of Sc (ASc) on MeHg-induced toxicity in rats. Two-day-old rats (P2) received a single dose of MeHg (10 mg/kg) and two doses of ASc (0.9 mg/kg) per os. After two days, the effects of the treatment were investigated in the cerebral cortex, hippocampus, kidney, liver and urine samples. Our results demonstrated that N-acetyl-β-D: -glucosaminidase (NAG) activity in the kidney and urine, the lipid peroxidation levels in the liver and kidney samples, as well as the adenosine deaminase (ADA) activity in the hippocampus, kidney and liver were higher in MeHg-group when compared to the control group. The administration of ASc reverted the toxic effects of MeHg. It is noteworthy to observe that the main compounds present in the ASc, as gallic acid (the major component), chlorogenic acid and rutin, might be the responsible for such benefit, since they were found to display antioxidant properties.