The aim of this study was to investigate hydrogen mobility within innate and demineralized human dentine. Dentine sections from extracted human molars, demineralized or not, were analyzed by combining neutron spectroscopy with thermal analysis. For the thermal analysis of the samples, differential scanning calorimetry and thermal gravimetric analysis, coupled with Fourier transform infrared spectroscopy, were performed. The hydrogen dynamics of water, collagen, and hydroxyl groups present in the samples were investigated via neutron spectroscopy. From the mass loss observed from the thermogravimetric analysis curves up to 600 °C, the same amount of organic content is identified in the samples. From the differential scanning calorimetry curves, a higher change in enthalpy associated with the denaturation of collagen is registered in the demineralized dentine; that is, a structural change occurs in the collagen subsequent to demineralization. Since the intensity measured by neutron spectroscopy is dominated by the signal from hydrogen, in our samples—coming mostly from the bulk-like and loosely bound water as well as from the collagen itself—higher proton mobility within the demineralized dentine was detected when compared with innate dentine. In the demineralized dentine, this proton mobility amounts to 80%, while the remaining hydrogen accounts for a combination of 1) structural hydroxyls, as a result of the incomplete dissolution of the mineral phase by acid etching, and 2) hydrogen tightly bound in the collagen structure. By combining neutron spectroscopy with the calorimetry data, our findings support the idea that hydroxyapatite protects the collagen in innate dentine. Demineralized dentine, however, acts as a sponge where free bulk-like water is trapped.