Synthetic pentlandite (Fe4.5Ni4.5S8) is a promising electrocatalyst for hydrogen evolution, demonstrating high current densities, low overpotential, and remarkable stability in bulk form. The depletion of sulfur from the surface of this catalyst during the electrochemical reaction has been proposed to be beneficial for its catalytic performance, but the role of sulfur vacancies and the mechanism determining the reaction kinetics are still unknown. We have performed electrochemical operando studies of the vibrational dynamics of pentlandite under hydrogen evolution reaction conditions using 57Fe nuclear resonant inelastic X-ray scattering. Comparing the measured Fe partial vibrational density of states with density functional theory calculations, we have demonstrated that hydrogen atoms preferentially occupy substitutional positions replacing pre-existing sulfur vacancies. Once all vacancies are filled, the protonation proceeds interstitially, which slows down the reaction. Our results highlight the beneficial role of sulfur vacancies in the electrocatalytic performance of pentlandite and give insights into the hydrogen adsorption mechanism during the reaction.