Climate change presents complex and wide-reaching threats to human health. A variable and changing climate can amplify and unmask ecological and socio-political weaknesses and increase the risk of adverse health outcomes in socially vulnerable regions. When natural disasters occur in such areas, underlying climatic conditions may amplify the public health crisis. We describe an emerging epidemic of Zika virus (ZIKV) in Ecuador following the 2016 earthquake, which coincided with an exceptionally strong El Niño event. We hypothesize that the trigger of a natural disaster during anomalous climate conditions and underlying social vulnerabilities were force multipliers contributing to a dramatic increase in ZIKV cases postearthquake.