Abstract Background Increase in total health expenditures is one of the main challenges of health systems worldwide, and its inequality is considered as a concern in global arena especially developing countries. This study aims to measure inequality in the distribution of selected indicators of national health accounts across the Iranian provinces. Methods In this study, the data on health financing agents from provincial health accounts from 2008 to 2016 were collected. Gini coefficient (GC) was used to measure inequality. The population and the number of service providers in each province were the bases to measure the GC. The Coefficient of Variation (CV) and the Rate Ratio (RR) were used to determine the dispersion and variation across the provinces. Disparity index was employed to measure the average deviation of the out-of-pocket (OOP) proportion from the desired OOP proportion presented in national development plans (NDPs) of Iran. Results The distribution of resources using both bases were unequal, especially in OOP, with the highest rate over the years studied, ranging from 0.50 to 0.59. The inequality in public resources was lower, with Health Insurance Organization dropping from 0.42 to 0.40 over the years. CV and RR also confirmed the inequality in health resources distribution. In the years 2014 and 2015, the lowest and highest levels were 0.22 and 0.39, respectively. The values of disparity index for OOP had a fluctuating trend ranging from 37.01 to 65.85%. Conclusion Inequality in the distribution of public health expenditures was moderate to high. Moreover, inequality in private health expenditures was higher than public one. Distribution of OOP spent by households at provincial level showed a high inequality. It is suggested that inequality measures to be considered in NDPs to illustrate how resources are distributed at the geographical level. NHA framework can help to provide robust evidence base for policymaking.