National and sub-national mortality, years of life lost due to premature mortality (YLLs), years lived with disability (YLDs) and disability-adjusted life years (DALYs) for household air pollution from solid cookfuel use (HAP) in Iran, 1990–2013 were estimated based on the Global Burden of Disease Study 2013 (GBD 2013). The burden of disease attributable to HAP was quantified by the comparative risk assessment method using four inputs: (1) exposure to HAP, (2) the theoretical minimum risk exposure level (TMREL), (3) exposure-response relationships of related causes (4) disease burden of related causes. All across the country, solid fuel use decreased from 5.26% in 1990 to 0.15% in 2013. The drastic reduction of solid fuel use leaded to DALYs attributable to HAP fell by 97.8% (95% uncertainty interval 97.7–98.0%) from 87,433 (51072–144303) in 1990 to 1889 (1016–3247) in 2013. Proportion of YLLs in DALYs from HAP decreased from 95.7% in 1990 to 86.6% in 2013. Contribution of causes in the attributable DALYs was variable during the study period and in 2013 was in the following order: ischemic heart disease for 43.4%, chronic obstructive pulmonary disease for 24.7%, hemorrhagic stroke for 9.7%, lower respiratory infections for 9.3%, ischemic stroke for 7.8%, lung cancer for 3.4% and cataract for 1.8%. Based on the Gini coefficient, the spatial inequality of the disease burden from HAP increased during the study period. The remained burden of disease was relatively scarce and it mainly occurred in seven southern provinces. Further reduction of the disease burden from HAP as well as compensation of the increasing spatial inequality in Iran could be attained through an especial plan for providing cleaner fuels in the southern provinces.