To investigate clinical features and therapeutic methods of late-onset central hypoventilation syndrome. A nine-year old boy was trachea-intubated and mechanically ventilated because of pneumonia, respiratory and heart failure and pulmonary hypertension. It was found that hard to extubate the patient as he was breathing normally while awake but had shallow breathing, oxygen desaturation and CO2 retention when falling asleep. Nocturnal polysomnography together with transcutaneous CO2 supported the diagnosis of central hypoventilation. The final diagnosis was late-onset congenital central hypoventilation syndrome as the patient gained weight rapidly since 3 years of age and the brain magnetic resonance imaging (MRI) and genetic screening were unremarkable. The patient was treated with bi-level positive air pressure ventilation via nasal mask which showed good oxygen saturation and CO2 dropped down. The follow up study done one year later showed normal brain MRI, relief of pulmonary hypertension and better CO2 level in both awaken and sleeping status. The late-onset congenital central hypoventilation syndrome in this case had onset of symptoms at 2 years of age, he had normal breathing while he was awake but had oxygen desaturation and CO2 retention during sleep, therefore, respiratory support is required in severe cases. Mechanical ventilation via tracheotomy and non-invasive ventilation via mask are the major choice.