Prion diseases are fatal, irreversible, and infectious neurodegenerative diseases caused by proteinase K‐resistant prion protein (PrPSc). Against PrPSc, several endogenous proteases involved in cellular degradation mechanisms can be activated to remove PrPSc. However, since PrPSc shows proteinase K resistance, we presumed that undegradable PrPSc induces positive feedback on the overactivation of the cellular degradation mechanisms and is correlated with proteolytic stress and exacerbation of the progression of prion diseases. We investigated the expression pattern of proteolytic stress‐related proteins in the brains of ME7 scrapie‐infected mice at 7 months postinfection and sporadic Creutzfeldt–Jakob disease (CJD) patients using western blotting and immunohistochemistry (IHC). In addition, we analyzed the 3D structure and binding complexes of prion protein (PrP) with nattokinase and lumbrokinase using in silico programs, including SWISS‐MODEL and HawkDock. To fundamentally reduce proteolytic stress by the degradation of PrPSc, we performed an in vitro evaluation of the PrPSc degradation abilities of fibrinolytic enzymes, including nattokinase and lumbrokinase. Furthermore, we assessed the protective effects of nattokinase and lumbrokinase in ME7 scrapie‐infected mice. We observed an abnormal accumulation of proteolytic stress‐related proteins, including CD10, cathepsin B, cathepsin D, and matrix metalloproteinase 9 (MMP9), in the brains of ME7 scrapie‐infected mice and sporadic CJD patients. In addition, we identified that nattokinase and lumbrokinase can stably bind to PrP. Furthermore, we identified significant in vitro degradation of PrPSc derived from ME7 scrapie‐infected mice and sporadic CJD patients by nattokinase and lumbrokinase. Last, we found in vivo protective effects of nattokinase and lumbrokinase against prion disease in ME7 scrapie‐infected mice. To the best of our knowledge, this is the first report on the identification of proteolytic stress‐related novel potential biomarkers and the therapeutic potential of nattokinase and lumbrokinase for prion diseases.