Purpose Vessel-encoded arterial spin labeling (VE-ASL) is able to provide noninvasive information about the contribution of individual arteries to the cerebral perfusion. The aim of this study was to compare VE-ASL to the diagnostic standard digital subtraction angiography (DSA) with respect to its ability to visualize vascular territories. Methods In total, 20 VE-ASL and DSA data sets of 17 patients with Moyamoya angiopathy with and without revascularization surgery were retrospectively analyzed. Two neuroradiologists independently assessed the agreement between VE-ASL and DSA using a 4-point Likert scale (no- very high agreement). Additionally, grading of the vascular supply of subterritories (A1-A2, M1-M6) on the VE-ASL images and angiograms was performed. The intermodal agreement was calculated for all subterritories in total and for the subdivision into without and after revascularization (direct or indirect bypass). Results There was a very high agreement between the VE-ASL and the DSA data sets (median = 1, modus = 1) with a substantial inter-rater agreement ( k w = 0.762 (95% CI 0.561–0.963)). The inter-modality agreement between VE-ASL and DSA in vascular subterritories was almost perfect for all subterritories ( k = 0.899 (0.865–0.945)), in the subgroup of direct revascularized subterritories ( k = 0.827 (0.738–0.915)), in the subgroup of indirect revascularized subterritories ( k = 0.843 (0.683–1.003)), and in the subgroup of never revascularized subterritories ( k = 0.958 (0.899–1.017)). Conclusion Vessel-encoded ASL seems to be a promising non-invasive method to depict the contributions of individual arteries to the cerebral perfusion before and after revascularization surgery.