One of the most tangible outcomes of climate change is change in the frequency of El Niño/La Niña events. They have a large impact on rainfall in the Western hemisphere, but their impact on tropical fauna is largely unknown. A decade long capture-mark-recapture study of the widespread Ecuadorian butterfly Nessaea hewitsoni (Felder & Felder) from an intact forest allowed us to analyze patterns of monthly and seasonal population dynamics before, during, and after an El Niño event. El Niño events did not affect long-term population size, but a 5-month delayed El Niño led to temporary emigration of females, with their subsequent return. Increased rainfall correlated with reduced survival in both sexes, but this effect was twice as strong in females. This investigation is the longest, continuous population study on any Neotropical insect species. Though we sampled on a modest scale, the magnitude of El Niño events suggests that our findings likely reflect insect population responses across a much larger portion of Amazonian forests.This study underscores the importance of analyzing multiple, interacting population parameters beyond local abundance in order to understand the biotic responses to El Niño and climate change in tropical systems. Had our analyses not included temporary emigration, no effect would have been detected because El Niño did not affect local population abundance.