Harlequin syndrome is a rare disease. It is probable that the unilateral facial sympathetic nerve dysfunction leads to contralateral facial flushing. A 28-year-old woman has been bothered with migraine with brainstem aura for over 6 years. Her right hemiface would flush and have paresthesia. After the headache, the sign would subside. Brain magnetic resonance imaging did not show any remarkable finding. There has been only two case reports of migraine with Harlequin syndrome in the literature. Herein we report the rare curiosity.