Little is understood about how the intrinsically disordered N-terminal region (NTR) of the prion protein modulates its misfolding and aggregation, which lead to prion disease. In this study, two pathogenic mutations, G113 V and A116 V in the palindromic region of the NTR, are shown to have no effect on the structure, stability or dynamics of native mouse prion protein (moPrP), but to nevertheless accelerate misfolding and oligomerization. For wt moPrP, misfolding and oligomerization appear to occur concurrently, while for both mutant variants, oligomerization is shown to precede misfolding. Kinetic hydrogen deuterium exchange-mass spectrometry experiments show that sequence segment 89-132 from the NTR becomes structured, albeit weakly, during the oligomerization of both mutant variants. Importantly, this structure formation occurs prior to structural conversion in the CTD, and appears to be the reason why the formation of misfolded oligomers is accelerated by the pathogenic mutations.