Estimation of the spatial and temporal trends of health impacts attributable to air pollution is an effective measure for evaluating implemented interventions. The aim of this study was to estimate the short-term mortality attributable to exposure to PM2.5 among individuals older than 30 years old in ten Iranian cities from March 2013 to March 2016 using the World Health Organization’s (WHO) AirQ+ software. Hourly concentrations of PM2.5 were acquired from the Department of Environment and Tehran Air Quality Control Company. Only stations with 75% and 50% of valid data were qualified for Tehran and other cities, respectively. The annual average PM2.5 concentrations in all ten of the cities were higher than the WHO guideline value of 10 µg m–3. The total number of attributable short-term deaths during the three-year period in these 10 cities was 3284 (95% CI: 1207–5244). The average daily premature deaths were calculated to be 3. The highest number of premature deaths within the three-year period was estimated to be 548 in Tehran, largely reflecting its population of nearly 9 million. The western and southern cities of Iran experience severe dust storms and showed a high estimated rate of death attributed to air pollution. The health impacts in all cities decreased in the third year compared to the first year except for Ahvaz, Khoram Abad, and Ilam. Governmental interventions need to be enforced more effectively to reduce the high level of adverse health impacts in Iran. Special considerations should be given to the air quality of cities affected by dust storms.