Migraine with aura (MwA) in pediatric patients is clinically frequent. Clinically complex symptoms need to be differentiated to exclude mimicking conditions.We hypothesize that MwA in children induces abnormalities readily visible in perfusion time to peak (TTP) maps as well as non-enhanced susceptibility weighted magnetic resonance imaging (SWI).Between 2010 and 2018, we retrospectively evaluated symptoms and imaging of consecutive pediatric patients18 years with MwA. We visually scored abnormalities on SWI and TTP maps in 12 regions of interest on both hemispheres on three axial slices, as normal, slightly, distinctly or severely abnormal.99 patients (69.7% female), mean age 14.07 y (±2.8) were included. Focally increased deoxygenation (FID) in SWI was present in 61.6%. FID on SWI was dominant for the left hemisphere (60.7% vs. 31.1%, (p .001)), and in 8.2% symmetric. Side of aura symptoms and contralateral hemispheric imaging alterations in patients with FID correlated significantly (p = .002.). 61 of 99 patients had perfusion MR and 59% of these patients showed focal increase of TTP. Age correlated significantly with FID in SWI (r = -.248, p = .013) and increase of TTP in perfusion (r = -.252, p = .05). Focal abnormalities correlated significantly between SWI and TTP maps. Brain regions most often abnormal were the temporal superior, occipital and fronto-parietal regions.This study provides confidence in recognizing FID, and linking FID in SWI to acute MwA in pediatric patients. FID phenomenon had a left hemispheric significant dominance, and can be found bilaterally.