As climate change worsens, the frequent occurrence of extreme drought events will further threaten the agricultural systems of all countries in the world. Kyrgyzstan is a country with agriculture and animal husbandry as its main industries, with a weak industrial base, and agriculture plays an important role in the national economy. Kyrgyzstan is located in Central Asia and suffers from a dry climate and frequent droughts. Thus, an integral analysis of the vulnerability of Kyrgyzstan’s agricultural system is of great significance for this country’s socio-economic stability. In this study, we comprehensively analyze the agricultural system drought vulnerability of Kyrgyzstan from three dimensions of sensitivity, adaptability and exposure. The results show that the areas of higher vulnerability in Kyrgyzstan’s agricultural system are distributed in the eastern mountainous, northwest and southwest areas. In addition, regions with low vulnerability are mainly concentrated in the central area. Kyrgyzstan has abundant water resources, but the supporting infrastructure construction is relatively backward. The imperfect irrigation facilities have greatly restricted the development of agriculture and have also increased the vulnerability of the agricultural systems. In the face of climate change, the region may face more severe drought disasters, so increasing infrastructure investment and building a complete irrigation system and water use plan are the keys to reducing the vulnerability of Kyrgyzstan’s agricultural system.