Mitochondrial diseases are a group of disorders caused by pathologic dysfunction of the mitochondrial respiratory chain that present with a wide range of clinical expression. Cardiorespiratory complications have previously been described in association with mitochondrial disease; however, pulmonary hypertension has rarely been reported. Pulmonary hypertension is characterized by elevated pulmonary arterial pressure and secondary right ventricular failure. It is a life-threatening condition with a poor prognosis if untreated. We report a case of 3-year-4-month-old boy who had mitochondrial A3243G point mutation with pulmonary hypertension. The unusual features of our case strengthen the concepts of pulmonary hypertension should be considered as another potential manifestation of mitochondrial disease.