Water resource management is critical for the economic development of the Democratic People’s Republic of Korea (DPRK), where runoff plays a central role. However, long and continuous runoff data at required spatial and temporal scales are generally not available in many regions in DPRK, the same as in many countries around the world. A common practice to fill the gaps is to use some kind of interpolation or data-infilling methods. In this study, the gaps in annual runoff data were filled using a distributed runoff map. A novel statistical–distributed model of average annual runoff was derived from 50 years’ observation on 200 meteorological observation stations in DPRK, considering the influence of climatic factors. Using principal component analysis, correlation analysis and residual error analysis, average annual precipitation, average annual precipitation intensity, average annual air temperature, and hot seasonal air temperature were selected as major factors affecting average annual runoff formation. Based on the water balance equation and assumptions, the empirical relationship for runoff depth and impact factors was established and calibrated. The proposed empirical model was successfully verified by 93 gauged stations. The cartography of the average annual runoff map was automatically implemented in ArcGIS. A case study on the Tumen River Basin illustrated the applicability of the proposed model. This model has been widely used for the development and management of water resources by water-related institutes and design agencies in DPRK. The limitation of the proposed model and future works are also discussed, especially the impacts of climate changes and topology changes and the combination with the physical process of runoff formation.