The protonation mechanism in Mn-doped CaZrO3 (CZM), which involves a direct hydrogen dissolution from the surrounding H2 gas, was investigated by thermogravimetry (TG) and X-ray absorption spectroscopy (XAS). The TG results implied the formation of oxygen vacancies in a H2 atmosphere. The Mn K-edge XAS spectra indicated a reduction of the Mn ions and local structure variations around the Mn ion, but the Zr K-edge spectra were independent of the surrounding atmosphere. The amount of oxygen vacancies was smaller with respect to the reduction of the Mn ions, suggesting direct dissolution of hydrogen. Unlike many typical perovskite-type proton conductors, protonation by direct dissolution of hydrogen and not hydration was the predominant reaction in Mn-doped CaZrO3. Our experimental results demonstrated that the hydration reaction was suppressed because the oxygen vacancy was stable in the distorted ZrO6 symmetry in the CaZrO3 crystal host, whereas protonation proceeded by the direct dissolution of hydrogen being stabilized near the Mn ions in the interstitial sites at the distorted MnO6 octahedral symmetry. The experimental results showed that the structural configurations around dopants play important roles in the stabilization of protons in perovskite-type CZM materials. We demonstrated a new group of proton conductors that can overcome issues with conventional proton conductors by utilizing the direct hydrogen dissolution reaction.