Mercury contamination affects many aquatic ecosystems1. The atmosphere is the main transport route for this toxicant2. According to aircraft measurements, the upper troposphere and lower stratosphere are depleted in gaseous elemental mercury3, 4 but enriched in oxidized, particle-bound mercury5, 6. It is therefore assumed that mercury is oxidized in the stratosphere, and then incorporated into stratospheric aerosols6. However, direct evidence for mercury oxidation in the stratosphere is missing. Here, we present simultaneous measurements of elemental and oxidized mercury concentrations in air of stratospheric origin, collected during an aircraft campaign over North America and Europe in 2010. We show that levels of oxidized mercury are strongly correlated with tracers of stratospheric air. Concentrations of total and elemental mercury, in contrast, are negatively correlated with these tracers. Together, the findings indicate that elemental mercury is oxidized in stratospheric air masses. We develop a numerical model of atmospheric mercury, based on the assumption that mercury is oxidized in the upper troposphere and lower stratosphere. The resultant vertical profiles—which depict a rapid decline in mercury concentrations with increasing stratospheric height—resemble those seen in other studies, and indicate that mercury has a relatively short stratospheric lifetime. We suggest that following oxidation, mercury is removed from the stratosphere by sedimentation and entrainment processes common to all stratospheric particles.