Atmospheric mercury (Hg) cycling is sensitive to climate-driven changes, but links with various teleconnections remain unestablished. Here, we revealed the El Niño–Southern Oscillation (ENSO) influence on gaseous elemental mercury (GEM) concentrations recorded at a background station in East Asia using the Hilbert–Huang transform (HHT). The timing and magnitude of GEM intrinsic variations were clearly distinguished by ensemble empirical mode decomposition (EEMD), revealing the amplitude of the GEM concentration interannual variability (IAV) is greater than that for diurnal and seasonal variability. We show that changes in the annual cycle of GEM were modulated by significant IAVs at time scales of 2–7 years, highlighted by a robust GEM IAV-ENSO relationship of the associated intrinsic mode functions. With confirmation that ENSO modulates the GEM annual cycle, we then found that weaker GEM annual cycles may have resulted from El Niño-accelerated Hg evasion from the ocean. Furthermore, the relationship between ENSO and GEM is sensitive to extreme events (i.e., 2015–2016 El Niño), resulting in perturbation of the long-term trend and atmospheric Hg cycling. Future climate change will likely increase the number of extreme El Niño events and, hence, could alter atmospheric Hg cycling and influence the effectiveness evaluation of the Minamata Convention on Mercury.