Climate change has altered global rainfall amounts and seasonality. Rainfed crops are particularly dependent on foreseeable rainfall, thus yields of maize, wheat and sorghum have decreased globally. Rainfed maize is the cornerstone of the agriculture in Mexico and the nutrition base of as many as twenty million people. Despite its relevance, the risk that climate change represents for this economic activity has not been studied in our country. We evaluated the link between rainfall variability and maize yields in Mexico across three different time periods: the present, the past 30 years and the remainder of this century (future) with RCPs scenarios. We found that rainfed agriculture was distributed as a function of the dry-season length, occurring in areas with a 4–9 months dry season, thus climate change may alter not only agricultural yields, but also the spatial distribution of land uses. There was a linear correlation (r = 0.45) between mean annual precipitation and rainfed maize production nationally for the period 1980–2012. The correlation was stronger (r = 0.91) during 2005–2012 when high-resolution data were available for the analysis. Correlation values were not homogeneously distributed within the country, although the minimum correlation was 0.35. In the future scenarios, yields were predicted to either not change or to decrease by as much as 10%. The strongest negative impacts were predicted across the Northeast and the South of the country, where yields declined by up to 30% in all scenarios.