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Hydrological drought plays an important role in planning and managing water resources systems to meet increasing water demands due to population growth. In this study, the effects of climate change on the hydrological drought characteristics of the Gharasu basin, as one of the major sub-basins of the Karkheh river basin, are investigated. This river basin has experienced severe droughts, and floods, in recent years. The uncertainties in projected drought conditions are characterized based on a suite of 34 general circulation models (GCMs). Based on hydrological simulations over the historical period, 12 GCMs are selected to estimate projected runoff values and the corresponding streamflow drought index (SDI) in the future period. The ‘run theory’ is applied to evaluate the drought characteristics under Representative Concentration Pathways (RCPs) 4.5 and 8.5 emission scenarios. Results show that uncertainties of drought projection under RCP8.5 are higher than under RCP4.5, where among different drought characteristics, the maximum uncertainty is detected for drought severity and maximum drought duration. Moreover, the uncertainty of drought projection in wet periods is greater than that in dry periods.