A factor constraining the elimination of dog-mediated human rabies is limited information on the size and spatial distribution of free-roaming dog populations (FRDPs). The aim of this study was to develop a statistical model to predict the size of free-roaming dog populations and the spatial distribution of free-roaming dogs in urban areas of Nepal, based on real-world dog census data from the Himalayan Animal Rescue Trust (HART) and Animal Nepal. Candidate explanatory variables included proximity to roads, building density, specific building types, human population density and normalised difference vegetation index (NDVI). A multivariable Poisson point process model was developed to estimate dog population size in four study locations in urban Nepal, with building density and distance from nearest retail food establishment or lodgings as explanatory variables. The proposed model accurately predicted, within a 95% confidence interval, the surveyed FRDP size and spatial distribution for all four study locations. This model is proposed for further testing and refinement in other locations as a decision-support tool alongside observational dog population size estimates, to inform dog health and public health initiatives including rabies elimination efforts to support the ‘zero by 30’ global mission.