Detection of subtle ischemic injuries in moyamoya disease may enable optimization of timing of revascularization surgery, and could potentially improve functional outcomes. Resting-state functional magnetic resonance imaging (rs-fMRI) is widely used to study functional organization of the brain, but it remains unclear whether rs-fMRI could elucidate distinct characteristics in moyamoya disease. Here, we aimed to determine changes in a conventional rs-fMRI measure and analyze any associations with clinical symptoms and cerebral hemodynamics. Thirty-one adults with moyamoya disease and 25 adult controls underwent rs-fMRI, in which we measured brain connectivity via temporal correlations of low-frequency BOLD signals. We identified the extent of between-group differences with multivoxel pattern analysis. Seed-based analysis was performed to determine associations with vascular lesions, symptoms, and regional cerebral blood flow (rCBF). There was significantly altered connectivity in the precentral gyrus, operculo-insular region, precuneus, cingulate cortex, and middle frontal gyrus in moyamoya disease. There was reduced connectivity in the left insula, left precuneus, right precentral, and right middle frontal regions, which form part of the salience, default mode, motor, and central executive networks, respectively. Patients with ischemic motor-related symptoms showed significantly decreased connectivity in precentral homotopic regions compared with those without, while there were no differences in vascular lesions or rCBF. Connectivity between the right occipital and left hippocampus was significantly associated with cognitive performance and posterior cerebral artery involvement. Our results demonstrate distinct alterations in the temporal correlations of low-frequency BOLD signals, predominantly in resting-state networks in moyamoya disease. Additionally, rs-fMRI measures were associated with ischemic motor-related symptoms and cognitive performance in the patients. Thus, rs-fMRI may offer a useful non-invasive method of acquiring additional information beyond cerebral perfusion as part of clinical investigations in patients with moyamoya disease.