Severe pulmonary arterial hypertension of systemic lupus erythematosus (SLE) in pediatrics is rarely seen, especially in boys. Sometimes SLE may only present as progressive fatigue and central cyanosis that may be diagnosed initially as cardiovascular diseases, which makes harder the diagnosis of SLE. We present a 13-year-old boy with a month of progressive fatigue and central cyanosis, diagnosed only as severe idiopathic pulmonary arterial hypertension. The boy was finally diagnosed as severe pulmonary arterial hypertension of systemic lupus erythematosus. Due to different choices of therapy, underlying cause of pulmonary arterial hypertension should be diagnosed and searched thoroughly.