Hydrogen is named as possible energy carrier for future energy systems. However, the impact of large-scale hydrogen use on the atmosphere is uncertain. Application of hydrogen in clean fuel cells reduces emissions of air pollutants, but emissions from hydrogen production and leakages of molecular hydrogen could influence atmospheric chemistry. This paper combines a global energy system model and a global atmospheric model to explore the range of impacts of hydrogen on atmospheric chemistry. We found that emissions of molecular hydrogen may range from 0.2 up to 10% (or 25–167 Tg hydrogen/yr) for a global hydrogen energy system. The lower end of this range would in fact be equal to current emissions from fossil fuel combustion. Hydrogen energy use leads to a clear decrease in emissions of carbon monoxide, nitrogen oxides and sulphur dioxide, but large-scale hydrogen production from coal may lead to net increase in emissions of nitrous oxide and volatile organic compound. Compared to a reference scenario, this would lead to positive impacts on surface concentrations of carbon monoxide, nitrogen oxides and ozone. However, if hydrogen leakage would not be minimised it leads to an increase in methane lifetimes and a decrease in stratospheric ozone concentrations.