The prevalence of migraine is higher in patients with atrial septal defect (ASD) (24.2%) than in the general Japanese population (9.4%). A few studies have reported that transcatheter closure of an interatrial shunt is known to attenuate migraine. We experienced hat surgical closure of the ASD improved migraine that was refractory to medication therapy. A 46-year-old man presented to a neurologist for evaluation of severe headache and was diagnosed with migraine. Brain magnetic resonance imaging (MRI) revealed evidence of previous multiple cerebral infarctions. Transesophageal echocardiography detected inferior sinus venosus-type ASD, and a bubble study showed the presence of a right-to-left shunt. Owing to the high index of clinical suspicion for paradoxical embolism via the ASD and the fact that percutaneous catheter closure was contraindicated for inferior sinus venosus-type ASD, we performed surgical closure of the ASD in this patient. The patient's migraine symptoms disappeared immediately after surgery, and no recurrence has been observed eight months after surgery. This is the first case report that surgical closure of ASD led to attenuate migraine. Our study highlights the association between right-to-left shunts and migraine, as well as the usefulness of the surgical closure of ASD as a therapeutic strategy for patients with migraine.