Abstract Background Countries aiming for malaria elimination need to define their malariogenic potential, of which measures of both receptive and current transmission are major components. As Namibia pursues malaria elimination, the importation risks due to cross-border human population movements with higher risk neighboring countries has been identified as a major challenge. Here we used historical and contemporary Plasmodium falciparum prevalence data for Namibia to estimate receptive and current levels of malaria risk in nine northern regions. We explore the potential of these risk maps to support decision-making for malaria elimination in Namibia. Methods Age-corrected geocoded community P. falciparum rate Pf PR 2-10 data from the period 1967–1992 (n = 3,260) and 2009 (n = 120) were modeled separately within a Bayesian model-based geostatistical (MBG) framework. A full Bayesian space-time MBG model was implemented using the 1967–1992 data to make predictions for every five years from 1969 to 1989. These maps were used to compute the maximum mean Pf PR 2-10 at 5 x 5 km locations in the northern regions of Namibia to estimate receptivity. A separate spatial Bayesian MBG was fitted to the 2009 data to predict current risk of malaria at similar spatial resolution. Using a high-resolution population map for Namibia, population at risk by receptive and current endemicity by region and population adjusted Pf PR 2-10 by health district were computed. Validations of predictions were undertaken separately for the historical and current risk models. Results Highest receptive risks were observed in the northern regions of Caprivi, Kavango and Ohangwena along the border with Angola and Zambia. Relative to the receptive risks, over 90% of the 1.4 million people across the nine regions of northern Namibia appear to have transitioned to a lower endemic class by 2009. The biggest transition appeared to have occurred in areas of highest receptive risks. Of the 23 health districts, 12 had receptive PA Pf PR 2-10 risks of 5% to 18% and accounted for 57% of the population in the north. Current PA Pf PR 2-10 risks was largely