Abstract Background Artificial intelligence (AI) predictive models have been used to estimate the risk of a certain outcome occurring, using all available variables. Methods Using AI methods we have developed a small area estimation (SAE) technique to estimate the prevalence of leisure-time physical activity (LTPA), or who practices 150 minutes of LTPA per week, in small areas, in Belo Horizonte, Brazil, between 2009 and 2018, by the usage of k-means clustering. The VIGITEL, national telephone survey of Risk Factors for non-communicable diseases, was the main source. We applied available data to estimate prevalence of LTPA in 3300 census tracts, aggregated in 150 Primary Health Care (PHC) areas. The prevalence of PA was analyzed between two time periods, due to the low number of census tract interviews. With the available data, we estimate vulnerability clusters, derived from a Health Vulnerability Index (IVS), for the city of Belo Horizonte, according to socioeconomic, sanitation and health indicators, which measure the percentage of the population living in areas of vulnerability in the city. The index main purpose is to support public policy implementation. Results Nine clusters were identified according to the Silhouette coefficient analysis, i.e.: low (LO-0, LO-1), medium (ME-0, ME-1), high (HI-0, HI-1, HI-2) and very high) vulnerability (VH-0, VH-1. The prevalence of physical activity ranged from 23.7% (worst prevalence), in area of high vulnerability cluster (VH-1) to 45.5% in a low-risk cluster (LO-1) in period from 2009 to 2014. The prevalence of physical activity increased to 31.4% (high vulnerability cluster) to 52.81% (low-risk cluster) from 2014 to 2018. Conclusions The use of AI to estimate the prevalence of physical activity in small areas proved to be effective and highlighted important differences in the city. Thus, national surveys, with a small number of interviews per census sector, can be used to predict risks and health outcomes for small areas. Key messages • The study highlights the importance of using artificial intelligence to predict estimates of risk factors for chronic non-communicable diseases in small geographic areas. • The study showed less physical activity (PA) in areas of greater vulnerability. This can support health promotion policies and programs that encourage PA.