Climate and infectious diseases each present critical challenges on a warming planet, as does the influence of climate on disease. Both are governed by nonlinear feedbacks, which drive multi-annual cycles in disease outbreaks and weather patterns. Although climate and weather can influence infectious disease transmission and have spawned rich literatures, the interaction between the independent feedbacks of these two systems remains less explored. Here, we demonstrate the potential for long-lasting impacts of El Niño–Southern Oscillation (ENSO) events on disease dynamics using two approaches: interannual perturbations of a generic SIRS model to represent ENSO forcing, and detailed analysis of realistic specific humidity data on an SIRS model with endemic coronavirus (HCoV-HKU1) parameters. Our findings reveal the importance of considering nonlinear feedbacks in susceptible population dynamics for predicting and managing disease risks associated with ENSO-related weather variations.