The accumulation of a large amount of amyloid-β (Aβ42) in brain neurons is one of the debilitating characteristics of Alzheimer's disease. In this study, we determined the effects of peroxisome proliferator-activated receptor alpha (PPARα) activation on neuronal degeneration using a model of Aβ42-induced cytotoxicity. We found that 0.5 μM Aβ42 induced DNA damage and apoptosis in NT2N cells after 6 h of treatment. Co-treatment of Aβ42-treated cells with Wy14643, a PPARα ligand, significantly increased cell viability after 24 h compared with cells treated with Aβ42 alone. There were no differences in the protein levels of caspase-3, Bcl-2/Bax or p53 between cells treated with Aβ42 alone and those treated with both Aβ42 and Wy14643. However, the addition of Wy14643 significantly suppressed the Aβ42-induced upregulation of Endo G and AIF protein levels. Immunohistochemical analyses further demonstrated that Wy14643 reduced the expression of Endo G and AIF translocated from the cytoplasm into the nucleus, which occurred concomitantly with the decrease in DNA damage in Aβ42-treated cells. Our data clearly show that PPARα activation prevents DNA damage and neuronal cell apoptosis by decreasing the expression and translocation of AIF/Endo G to the nucleus in a caspase-3- and p53-independent pathway in the NT2N cell model. This role of PPARα in promoting neuron survival suggests a possible clinical application in treating Aβ42-associated neurotoxicity in Alzheimer's disease.