Uganda is one of the poorest nations in the world. It is important to obtain accurate, timely data on socio-economic characteristics sub-nationally, so as to target poverty reduction strategies to those most in need. Many studies have demonstrated that nighttime lights (NTL) can be used to measure human activities. Nevertheless, the methods developed from these studies (1) suffer from coarse resolutions, (2) fail to capture the nonlinearity and multi-scale variability of geospatial data, and (3) perform poorly for agriculture-dependent regions. This study proposes a new enhanced light intensity model (ELIM) to estimate the gross domestic product (GDP) for sub-national units within Uganda. This model is developed by combining the NTL data from the Suomi National Polar-orbiting Partnership Visible Infrared Imaging Radiometer Suite (NPP-VIIRS), the population data from the Global Human Settlement Layer (GHSL), and information on agricultural production and market prices across several commodity types. This resulted in a gridded dataset for Uganda’s GDP at sub-national levels, to capture the spatial heterogeneity in the economic activity.