An assessment of climate change impacts on the habitat suitability of fish species is an important tool to improve the understanding and decision-making needed to reduce potential climate change effects based on the observed relationships of biological responses and environmental conditions. In this study, we use historical (2010–2015) environmental sea surface temperature (SST), upwelling index (UI), chlorophyll-a (Chl-a) and biological (i.e., anchovy adults acoustic presence) data (i.e., Maxent) to determine anchovy habitat suitability in the coastal areas off central-northern (25°S–32°S) Chile. Using geographic information systems (GIS), the model was forced by changes in regionalized SST, UI and Chl-a as projected by IPCC models under the RPC (i.e., RCP2.6, RCP4.5, RCP6.0 and RCP8.5) emissions scenarios for the simulation period 2015–2050. The model simulates, for all RCP scenarios, negative responses in anchovy presence, reflecting the predicted changes in environmental variables, dominated by a future positive (warming) change in SST and UI, and a decrease in chlorophyll-a (i.e., phytoplankton biomass). The model predicts negative changes in habitat suitability in coastal areas from north of Taltal (25°S) to south of Caldera (27°45′S) and in Coquimbo littoral zone (29°–30°12′S). The habitat suitability models and climate change predictions identified in this study may provide a scientific basis for the development of management measures for anchovy fisheries in the coastal areas of the South American coast and other parts of the world.