Global measurements of atmospheric methane (CH4) concentrations continue to show large interannual variability whose origin is only partly understood. Here we quantify the influence of the El Niño–Southern Oscillation (ENSO) on wetland CH4 emissions, which are thought to be the dominant contributor to interannual variability of the CH4 sources. We use a simple wetland CH4 model that captures variability in wetland extent and soil carbon to model the spatial and temporal dynamics of wetland CH4 emissions from 1950–2005 and compare these results to an ENSO index. We are able to explain a large fraction of the global and tropical variability in wetland CH4 emissions through correlation with the ENSO index. We find that repeated El Niño events throughout the 1980s and 1990s were a contributing factor towards reducing CH4 emissions and stabilizing atmospheric CH4 concentrations. An increase in emissions from the boreal region would likely strengthen the feedback between ENSO and interannual variability in global wetland CH4 emissions. Our analysis emphasizes that climate variability has a significant impact on wetland CH4 emissions, which should be taken into account when considering future trends in CH4 sources.