Drought has devastating impacts on agriculture and other ecosystems, and its occurrence is expected to increase in the future. However, its spatiotemporal impacts on net primary productivity (NPP) in Mongolia have remained uncertain. Hence, this paper focuses on the impact of drought on NPP in Mongolia. The drought events in Mongolia during 2003–2018 were identified using the Moderate Resolution Imaging Spectroradiometer (MODIS) normalized difference vegetation index (NDVI). The Boreal Ecosystem Productivity Simulator (BEPS)-derived NPP was computed to assess changes in NPP during the 16 years, and the impacts of drought on the NPP of Mongolian terrestrial ecosystems was quantitatively analyzed. The results showed a slightly increasing trend of the growing season NPP during 2003–2018. However, a decreasing trend of NPP was observed during the six major drought events. A total of 60.55–87.75% of land in the entire country experienced drought, leading to a 75% drop in NPP. More specifically, NPP decline was prominent in severe drought areas than in mild and moderate drought areas. Moreover, this study revealed that drought had mostly affected the sparse vegetation NPP. In contrast, forest and shrubland were the least affected vegetation types.