Climate-related phenomena in Peru have been slowly but continuously changing in recent years beyond historical variability. These include sea surface temperature increases, irregular precipitation patterns and reduction of glacier-covered areas. In addition, climate scenarios show amplification in rainfall variability related to the warmer conditions associated with El Niño events. Extreme weather can affect human health, increase shocks and stresses to the health systems, and cause large economic losses. In this article, we study the characteristics of El Niño events in Peru, its health and economic impacts and we discuss government preparedness for this kind of event, identify gaps in response, and provide evidence to inform adequate planning for future events and mitigating impacts on highly vulnerable regions and populations. This is the first case study to review the impact of a Coastal El Niño event on Peru’s economy, public health, and governance. The 2017 event was the third strongest El Niño event according to literature, in terms of precipitation and river flooding and caused important economic losses and health impacts. At a national level, these findings expose a need for careful consideration of the potential limitations of policies linked to disaster prevention and preparedness when dealing with El Niño events. El Niño-related policies should be based on local-level risk analysis and efficient preparedness measures in the face of emergencies.