The conversion of Indonesian tropical peatlands has been associated with the recurring problems of peatland fires and smoke affecting humans and the environment. Yet, the local government and public in the affected areas have paid little attention to the impacts and costs of the poor air quality on human health. This study aims to analyse the long-term health impacts of the peat smoke exposure to the local populations. We applied the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to determine the smoke dispersion and the associated PM2.5 concentrations of the resulted plumes from the fire hotspots in the deep and shallow peatlands in Central Kalimantan, Indonesia, that occurred during a 5-year period (2011–2015). We subsequently quantified the long-term health impacts of PM2.5 on the local people down to the village level based on the human health risk assessment approach. Our study shows that the average increase in the annual mean PM2.5 concentration due to peatland fires in Central Kalimantan was 26 μg/m3 which is more than twice the recommended value of the World Health Organisation Air Quality Guidelines. This increase in PM2.5 leads to increased occurrence of a range of air pollution–related diseases and premature mortality. The number of premature mortality cases can be estimated at 648 cases per year (26 mortality cases per 100,000 population) among others due to chronic respiratory, cardiovascular and lung cancer. Our results shed further light on the long-term health impacts of peatland fires in Indonesia and the importance of sustainable peatland management.