BackgroundSecondary polycythemia is considered the usual complication of chronic hypoxia. It can theoretically increase the oxygen-carrying capacity, but this adaptive trait has a deleterious effect because the blood viscosity increases, which can induce significant morbidity and mortality, such as stroke and myocardial infarction.Case presentationA 55-year-old man with a history of a congenitally small main pulmonary artery presented to the emergency department with sustained unsteady walking, dizziness and vertigo. Evaluation revealed elevated hemoglobin and superior posterior circulation cerebral artery thrombosis. The patient was treated with high flux inhalation of oxygen and anti-platelet aggregation.ConclusionsThe involvement of cerebral vessels has rarely been reported in chronic hypoxia cases. The present case is the first case of superior posterior circulation cerebral artery thrombosis due to chronic hypoxia in a patient with a congenitally small main pulmonary artery. This case demonstrates the importance of recognizing some chronic diseases that can lead to hypoxia and secondary polycythemia thereby leading to hypercoagulable state and subsequent thrombosis.