Blood oxygenation level dependent (BOLD)–based functional MRI (fMRI) is a widely utilized neuroimaging technique for mapping brain function. Hematocrit (HCT), a global hematologic marker of the amount of hemoglobin in blood, is known to impact task-evoked BOLD activation. Yet, its impact on resting-state fMRI (R-fMRI) measures has not been characterized. We address this gap by testing for associations between HCT level and inter-individual variation in commonly employed R-fMRI indices of intrinsic brain function from 45 healthy adults. Given known sex differences in HCT, we also examined potential sex differences. Variation in baseline HCT among individuals were associated with regional differences in four of the six intrinsic brain indices examined. Portions of the default (anterior cingulate cortex/medial prefrontal cortex: ACC/MPFC), dorsal attention (intraparietal sulcus), and salience (insular and opercular cortex) network showed relationships with HCT for two measures. The relationships within MPFC, as well as visual and cerebellar networks, were modulated by sex. These results suggest that inter-individual variations in HCT can serve as a source of variations in R-fMRI derivatives at a regional level. Future work is needed to delineate whether this association is attributable to neural or non-neuronal source of variations and whether these effects are related to acute or chronic differences in HCT level.