This study aimed to observe the changes of venous continuity using the susceptibility weighted imaging-minimum intensity projection (SWI-MinIP) images in children with primary headache. The headache types were classified following the International Headache Society's diagnostic criteria. Patients with secondary headaches were excluded. The presence of asymmetric vasculature in SWI-MinIP images was visually assessed. Moreover, the relationship between headache patterns and asymmetric hypointense signals was analyzed. In this single-center, retrospective study from 2016 to 2020, among 251 cases of primary headache (male/female, 108/143; mean age, 11.4 ± 4.0years), 137 (54.6%), 75 (29.9%), and 39 (15.5%) patients had migraine, tension-type headache, and other primary headaches, respectively. On SWI-MinIP images, 14 (5.6%) patients showed an asymmetric venous pattern. All patients with SWI-MinIP asymmetry were included in the migraine group, accounting for 10.2% of patients with migraine. Five (35.7%) and nine (64.3%) patients were included in the aura and non-aura groups, respectively, without a significant difference in the frequency of asymmetric hypointense signals between the two groups (p = 0.325). All 14 patients with asymmetric hypervascularity had brain MRI within 12h of headache onset. Ten (71.4%) of the 14 patients showed consistency between the laterality of headache and the hemisphere of predominant vascularity in SWI-MinIP. Patients with migraine had increased cerebral venous perfusion in the most involved region of the headache on the SWI-MinIP view on a 3.0T scanner, which can be used as a qualitative indicator with low sensitivity and high specificity for the diagnosis of primary headache in the acute phase (< 12h).