Methylmercury is a major environmental pollutant that exhibits neurotoxicity. We previously reported that proteolytic systems such as the ubiquitin–proteasome system (UPS) and autophagy are involved in methylmercury toxicity. It is known that the intercellular level of PTEN, a phosphatase involved in autophagy inhibition, is regulated by the UPS. In this study, we coincidentally found that the PTEN level was decreased by methylmercury in the lysate solubilized with RIPA buffer containing 0.1% sodium dodecyl sulfate (SDS). However, the decrease in PTEN level caused by methylmercury was scarcely observed in RIPA buffer containing 2% SDS. These results suggest that methylmercury lowers the solubility of PTEN protein. Moreover, phosphorylation of Akt, a protein kinase that is negatively controlled via PTEN, was accelerated in accordance with a decrease in PTEN protein solubility. This suggests that methylmercury may inhibit PTEN activity by decreasing its solubility. Moreover, PTEN overexpression confers resistance to methylmercury in SH-SY5Y neuroblastoma cells. These results suggest that PTEN is a novel factor involved in reducing methylmercury toxicity and that methylmercury inhibits PTEN activity by decreasing the solubility of PTEN protein, thereby increasing cytotoxicity.