Abstract Despite their pronounced climate impacts, the physical processes that control the frequency of multiyear El Niño events remain incompletely understood. Using an Interactive Ensemble (IE) coupling strategy, we find that atmospheric noise forcing plays an important role in modulating the frequency of multiyear El Niño events. When thermocline‐related stochastic forcing is stronger, equatorial warm‐water volume is less effectively discharged after the first El Niño peak, increasing the likelihood that positive recharge persists into the following year. Sensitivity experiments with the Stochastic Recharge Oscillator model show that a larger diagnosed σh ${sigma }_{h}$ (the amplitude of wind‐stress–driven atmospheric noise forcing on thermocline‐depth anomalies) is systematically associated with a higher frequency of multiyear El Niño events. These results reveal a previously underrecognized pathway through which stochastic atmospheric variability modulates the persistence of El Niño events.