OBJECTIVE: Although the cause of Alzheimer's disease (AD) is still controversial, it is generally accepted that neuroinflammation plays a key role in AD pathogenesis. Thus, regulating the polarization of microglia will help in recovering from AD since microglia can be polarized into classical M1 and alternative M2 phenotypes, M1 microglia leading to neuroinflammation and M2 microglia acting as anti-inflammatory effectors. Our previous study demonstrated that eicosapentaenoic acid (EPA), an essential n-3 polyunsaturated fatty acid, may modulate glial cell activity and functions, but it is not clear whether EPA plays a role in microglial polarization. Here, we aimed to test the hypothesis that EPA may regulate the polarization of microglia and subsequently alleviate neuroinflammation and neuronal damage. METHODS: Male C57BL/6 mice were fed an EPA-supplemented diet or a palm oil-supplemented diet for 42 days. On day 28 of diet feeding, the mice received a single intracerebroventricular injection of β-peptide fragment 1-42(Aβ1-42) or saline. The polarization of M1 and M2 microglia was evaluated by western blot using the respective markers. Changes in inflammatory cytokine mRNA levels were examined using real-time PCR. Neurological deficits were analysed using the Morris water maze and TdT-mediated dUTP Nick-End Labeling (TUNEL) assays. RESULTS: EPA supplementation effectively reversed the increasing trend of M1 microglial markers and the decreased expression of M2 microglial markers in the hippocampus mediated by Aβ1-42 and normalized the Aβ-induced upregulation of proinflammatory cytokines and the downregulation of anti-inflammatory factors. Consistent with these findings, EPA significantly improved cognitive function and inhibited apoptotic neuronal death in the hippocampus. CONCLUSION: These results demonstrated that EPA appears to have potential effects on regulating microglial polarization, which contributes to alleviating neuroinflammation and may have beneficial effects for preventing and treating AD.