Previous studies show that nitrogen gas plasma generated by a fast-pulsed power supply using a static induction thyristor has both virucidal and bactericidal effects. In this study, nitrogen gas plasma was further evaluated for its potential effects on prions, which are well known to be the most resistant pathogen to both chemical and physical inactivation. Aliquots (10 μL) of mouse brain homogenate infected with Chandler scrapie prion were spotted onto cover glasses and subjected to nitrogen gas plasma. Treated samples were recovered and subjected to further analyses. Control prion samples were prepared in exactly the same way but without plasma treatment. Protein misfolding cyclic amplification (PMCA) showed that nitrogen gas plasma treatment at 1.5 kilo pulse per second for 15 or 30 min caused a reduction in the in vitro propagation level of PrPres (proteinase K-resistant prion protein), which was used as an index of abnormal prion protein (PrPSc). Moreover, mice injected with prion treated with plasma for 30 min showed longer survival than mice injected with control prion, indicating that nitrogen gas plasma treatment decreased prion infectivity. Altogether, these results suggest that nitrogen gas plasma treatment can inactivate scrapie prions by decreasing the propagation activity and infectivity of PrPSc.