The El Niño–Southern Oscillation (ENSO) affects the tropospheric concentrations of many trace gases. Here we investigate the ENSO influence on mercury concentrations measured in the upper troposphere during Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrumented Container flights and at ground at Cape Point, South Africa, and Mace Head, Ireland. Mercury concentrations cross-correlate with Southern Oscillation Index (SOI) with a lag of 8 ± 2 months.