A switch from a fossil fuel to a hydrogen-based energy system could cause significant changes in the magnitude and composition of anthropogenic emissions. Model simulations suggest the most significant impact of these emission changes would occur in the troposphere, affecting OH. This impact is dependent upon the magnitude and nature of trade-offs in changing fossil fuel use. In the stratosphere, changes in water vapour resulting from expected increases in surface molecular hydrogen emissions via leaks occurring during production, transport and storage, are found to be significantly smaller than previous estimates. We conclude that the expected increase in molecular hydrogen emissions is unlikely to have a substantial impact on stratospheric ozone, certainly much smaller than the ozone changes observed in the last two decades.