Breathing disturbances are often a major clinical concern during wakefulness of classic form of Rett syndrome, but data for atypical forms are lacking. We report the case of a 20-month-old female affected by the congenital variant of Rett syndrome, that is characterized by severe hypotonia and neurodevelopment impairment. She presented hypoventilation, persistent periodic breathing and sustained desaturation during sleep time, without obstructive nor central events; pulse oximetry and capnography during wakefulness were strictly normal. To the best of our knowledge, this is the first case of Rett syndrome presenting hypoventilation. Hypotonia may play a major role in the genesis of hypoventilation and hypoxemia in our patient. Non-invasive ventilation led to quality-of-life improvements. Thus, we suggest screening patients with congenital Rett variant through transcutaneous bedtime carbon dioxide and oxygen monitoring. Moreover, in our case, assisted control mode was a breakthrough to achieve adequate ventilation.