Objective A child presenting with a first attack of migraine with aura usually undergoes magnetic resonance imaging (MRI) to rule out stroke. The purpose of this study was to report vascular and brain perfusion findings in children suffering from migraine with aura on time-of-flight MR angiography (TOF-MRA) and MR perfusion imaging using arterial spin labelling (ASL). Methods We retrospectively included all children who had undergone an emergency MRI examination with ASL and TOF-MRA sequences for acute neurological deficit and were given a final diagnosis of migraine with aura. The ASL perfusion maps and TOF-MRA images were independently assessed by reviewers blinded to clinical data. A mean cerebral blood flow (CBF) value was obtained for each cerebral lobe after automatic data post-processing. Results Seventeen children were finally included. Hypoperfusion was identified in one or more cerebral lobes on ASL perfusion maps by visual assessment in 16/17 (94%) children. Vasospasm was noted within the intracranial vasculature on the TOF-MRA images in 12/17 (71%) children. All (100%) of the abnormal TOF-MRA images were associated with homolateral hypoperfusion. Mean CBF values were significantly lower ( P < 0.05) in visually hypoperfused lobes than in normally perfused lobes. Conclusion ASL and TOF-MRA are two totally non-invasive, easy-to-use MRI sequences for children in emergency settings. Hypoperfusion associated with homolateral vasospasm may suggest a diagnosis of migraine with aura.