Previous studies have shown that hypoxic preconditioning attenuates prion-mediated neurotoxicity by upregulating hypoxia inducible factor-1α (HIF-1α). However, the mechanisms behind the HIF-1α-mediated neuroprotective effects in neurodegenerative disorders, including prion diseases, are unclear. It is well known that HIF-1α regulates Wnt/β-catenin signaling and that β-catenin protects neurons against misfolded protein-mediated disorders, including Alzheimer's and Parkinson's disease by preventing mitochondrial malfunction. Thus, we hypothesized that the mechanisms responsible for HIF-1α-mediated neuroprotection are associated with β-catenin activation induced by the regulation of mitochondrial function. We used the SH-SY5Y human neuroblastoma cell line and treated the cells with melatonin and then exposed them to the prion protein, PrP, or the β-catenin inhibitor, ICG-001. TUNEL assay was used to measure apoptosis. β-catenin expression measured by western blot analysis. The results revealed that HIF-1α prevented prion protein (PrP) (106-126)-induced neurotoxicity by activating β-catenin. Moreover, HIF-1α-induced β-catenin activation prevented the PrP (106-126)-induced mitochondrial damage under hypoxic conditions, as evidenced by the higher mitochondrial transmembrane potential values in the cells exposed to hypoxic conditions. These results indicate that the regulation of β-catenin activation by HIF-1α may be a therapeutic strategy for prion-mediated disorders.