Regional disparities are among the major challenges to achieving balanced development and reducing spatial inequalities. This study aims to assess and analyze regional disparities among the counties of the Zagros region and examine their changes across three time periods: 1996, 2006, and 2016. In this study, 26 economic, social, and environmental indicators were examined for 43 counties in the Zagros region. Following data standardization, factor analysis was used to identify the main dimensions of regional disparities, the F'ANP model was employed to determine the weights of the indicators, and cluster analysis was used to classify the counties. The results were also spatially represented using ArcGIS. The factor analysis results showed that the examined indicators could be grouped into seven main factors, namely employment and industry, public services, health and education, employment and medical services, industrial energy consumption, culture and public information, and environment and urban infrastructure. The results of the F'ANP model also indicated differences in the relative importance of the indicators, with indicators related to resource and energy consumption as well as some public and cultural services showing greater importance within the integrated structure. The results of county classification indicated that regional disparities experienced relative but uneven improvement over the study period. While the situation of some counties improved across different factors, others remained at lower levels. Furthermore, the noticeable differences between some provincial centers and their surrounding counties indicate the persistence of spatial and structural inequalities in the region. Therefore, sustainable reduction of regional disparities in the Zagros region requires targeted attention to less-developed counties and more balanced distribution of infrastructure, services, and regional investments.