Introduction Despite progress towards the Joint United Nations Programme on HIV/AIDS 95-95-95 targets, South Africa is still suffering from one of the largest HIV epidemics globally. In this study, we generated high-resolution HIV prevalence maps and identified people living with HIV (PLHIV) in underserved areas to provide essential information for the optimal allocation of HIV-related services.Methods The data come from the South Africa Demographic and Health Survey conducted in 2016 and spatial variables from other published literature. We produced high-resolution maps of HIV prevalence and underserved areas, defined as a greater than 30 min travel time to the nearest healthcare facility. Using these maps and the population density, we mapped PLHIV and the PLHIV within underserved areas for 30, 60 and 120 min thresholds.Results There was substantial geographic variation in HIV prevalence, ranging from 1.4% to 24.2%, with a median of 11.5% for men, and from 2.1% to 48.1%, with a median of 20.6% for women. Gauteng province showed the highest density for both HIV prevalence and PLHIV. 80% of all areas in the country were identified as underserved areas (30 min threshold), which contained more than 16% and 20% of the total men and women living with HIV, respectively. KwaZulu-Natal province had the largest number of PLHIV in underserved areas (30 min threshold) and showed less than one healthcare facility per 1000 PLHIV.Conclusion Our study showed extensive spatial variation of HIV prevalence and significant numbers of PLHIV in underserved areas in South Africa. Moreover, we identified locations where HIV-related services need to be intensified to reach the ~1.5 million PLHIV in underserved areas, particularly in KwaZulu-Natal province, with less than one healthcare facility per 1000 PLHIV.Data are available in a public, open-access repository. The data that support the findings of this study are available from the Demographic and Health Surveys (http://www.measuredhs.com), but restrictions apply to the availability of these data, which were used under licence for the current study and so are not publicly available. However, data are available from the authors on reasonable request and with the permission of Demographic and Health Surveys. We sought and were granted permission to use the core data set for this analysis by Measure DHS.