For policies and programs aiming at reducing climate risk, it is important to obtain vulnerability information at the sub-national level to identify hotspots. For the case of Costa Rica, no sub-national climate vulnerability index exists to date. To fill this gap, we constructed a climate vulnerability index at the canton level. We ground our work in the conceptual framework that vulnerability is a function of exposure, sensitivity, and adaptive capacity. Making extensive use of geographic information systems and publicly available data, we constructed 13 spatial layers to reflect the multi-dimensionality of vulnerability. Layers reflect for example, changes in climatic extremes, flood risk, vegetation cover, access to infrastructure (road density) and health services (distance to hospitals), as well as various socioeconomic (wealth level, employment rates, remittances, literacy rate) and demographic (infant mortality) characteristics. Following normalization, we constructed an inverse variance weighted index of canton-level climate vulnerability. We confirmed the validity of our climate vulnerability index through correlation with disaster damage data. We find the strongest climate vulnerability not only in the rural, agricultural producing border cantons (Los Chiles, Matina, Talamanca, Buenos Aires), but also for a few central urban cantons (Tibas, San Jose). Projects and interventions in these hot spot cantons may reduce sensitivity through strengthening hydrological infrastructure and economic development, while adaptive capacity may be improved through addressing barriers of remittance transfer, and via public health programs.