Background <p>Prion diseases are a group of incurable and fatal neurodegenerative disorders characterized by neuronal cell death. Calcineurin and autophagy induce neurotoxicity by prion proteins, which may have therapeutic benefits by inhibiting calcineurin and autophagy. Baicalein is known to have neuroprotective effects against calcium-dependent cell death in aging and neurodegenerative diseases.</p> Methods <p>Western blot analysis was used to detect the expression levels of autophagy flux pathway. Transmission electron microscopy (TEM) was used to detect autophagy flux. A calcineurin cellular activity assay kit was used to examine calcineurin activity. Fluo-4 was used to measure calcium inside living cells by confocal microscope.</p> Results <p>In the present study, it was confirmed whether baicalein reduces cytotoxicity caused by prion protein, and whether it regulates calcium and calcineurin was investigated. As a result, it was confirmed that baicalein has a protective effect by reducing the cytotoxicity increased by the prion protein. Baicalein showed a protective effect by reducing the activity of calcium and calcineurin by the prion protein. Next, we investigated whether baicalein is involved in regulating the calcineurin-autophagy pathway. As a result, autophagy activated by the prion protein was also reduced by baicalein, and it was confirmed that the protective effect of baicalein by the prion protein occurred through autophagy.</p> Conclusions <p>This conclusion suggests that neurotoxicity by prion protein occurs through calcineurin and autophagy and that baicalein has neuroprotective effects through these mechanisms.</p>