Speculation exists that the emergence of Zika virus (ZIKV) as a public health emergency in Latin America and the Caribbean (LAC) is partially related to high temperatures associated with the 2015-2016 El Nino event. Analysis of related flaviviruses -such as dengue and chikungunya, which are transmitted by the same vectors- suggests that ZIKV is sensitive to climate. Quantifying the climate contribution to ZIKV transmission is an important step in better understanding the conditions conducive to the 2014-2016 epidemic, and permits the development of climate-informed short- and long-term strategies for ZIKV prevention and control. Using a novel timescale-decomposition methodology, here we demonstrate that extreme climate anomalies observed in most parts of South America during the current epidemic are not caused exclusively by El Nino or climate change -as speculated-, but are the result of a particular combination of climate signals acting at multiple timescales. In Brazil, the heart of the epidemic, we find that dry conditions present during 2013-2015 are explained primarily by year-to-year variability superimposed on decadal variability, but with little contribution of long-term trends. In contrast, the extreme warm temperatures of 2014-2015 resulted from the compound effect of climate change, decadal and year-to-year climate variability. The increasingly probable 2016-2017 La Nina suggests that ZIKV response strategies adapted for a drought context in Brazil may need to be revised to accommodate the likely return of heavy rainfall. Temperatures are likely to remain warm given the importance of long term and short term trends.