The reduction of emissions of mercury is a declared aim of the Minamata Convention, a UN treaty designed to protect human health and the environment from adverse effects of mercury. To assess the effectiveness of the convention in the future, better constraints about the current mercury emissions is a premise. In our study, we applied a top-down approach to quantify mercury emissions on the basis of atmospheric mercury measurements conducted at the remote high altitude monitoring station Jungfraujoch, Switzerland. We established the source-receptor relationships and by the means of atmospheric inversion we were able to quantify spatially resolved European emissions of 89 ± 14 t/a for elemental mercury. Our European emission estimate is 17% higher than the bottom-up emission inventory, which is within stated uncertainties. However, some regions with unexpectedly high emissions were identified. Stationary combustion, in particular in coal-fired power plants, is found to be the main responsible sector for increased emission estimates. Our top-down approach, based on measurements, provides an independent constraint on mercury emissions, helps to improve and refine reported emission inventories, and can serve for continued assessment of future changes in emissions independent from bottom-up inventories.