Cluster-like headache has been described as a secondary to several intracranial pathology. More than half of patients with lateral medullary infarction develop headache, but headache associated with autonomic symptom is very rare. We report the case of a 61-year-old man with chronic cluster-like headache associated with acute lateral medullary infarction. Damage of lateral medulla leads to imbalance of the autonomic system. Activated trigemino-autonomic system might be contributing factors of this headache.