Estimation of the spatial and temporal trends of health impacts attributable to air pollution is an effective measure to evaluate implemented interventions. The aim of this study was to estimate the short-term mortality attributed to exposure to PM2.5 among individuals older than 30 years old in 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 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 of PM2.5 concentrations in all the ten cities were higher than the WHO guideline value of 10 µg m–3. Total attributable short-term deaths during the three-year period in these 10 cities were 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 mostly its population of nearly 9 million. The western and southern cities of Iran have occurrences of severe dust storms and showed high estimated rate of death attributed to air pollution. The health impacts in all cities have decreased in the third year compared to the first year except for Ahvaz, Khoram Abad, and Ilam. Government 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.