Thunderclap headache is well known to be a presenting feature of a variety of causal events. Indeed, a primary form is considered in the International Classification of Headache Disorders-II, but such diagnosis must be made only after exclusion of a possible secondary cause. We report a case of late-onset idiopathic aqueductal stenosis presenting with thunderclap headache, in the absence of abnormal neurological findings or indirect signs of raised intracranial pressure. The patient recovered completely after endoscopic third ventriculostomy. This case indicates primary aqueduct stenosis as a possible, never previously reported, cause of thunderclap headache.