The Earth’s core–mantle boundary presents a dramatic change in materials, from silicate to metal. While little is known about chemical interactions between them, a thin layer with a lower velocity has been proposed at the topmost outer core (Eʹ layer) that is difficult to explain with a change in concentration of a single light element. Here we perform high-temperature and -pressure laser-heated diamond-anvil cell experiments and report the formation of SiO2 and FeHx from a reaction between water from hydrous minerals and Fe–Si alloys at the pressure–temperature conditions relevant to the Earth’s core–mantle boundary. We suggest that, if water has been delivered to the core–mantle boundary by subduction, this reaction could enable exchange of hydrogen and silicon between the mantle and the core. The resulting H-rich, Si-deficient layer formed at the topmost core would have a lower density, stabilizing chemical stratification at the top of the core, and a lower velocity. We suggest that such chemical exchange between the core and mantle over gigayears of deep transport of water may have contributed to the formation of the putative Eʹ layer.