The association between spina bifida, specifically myelomeningocele, and autonomic dysfunction is known although rare. This case highlights the severe respiratory compromise that can occur in paediatric patients secondary to myelomeningocele. We describe a case of a neonate who experienced profound respiratory dysfunction following a successful lumbosacral myelomeningocele repair on Day 1 of life, on the background of a prenatal diagnosis of Arnold-Chiari Type II malformation and congenital hydrocephalus. In addition, the patient was found to have an incidental choroid plexus papilloma which was resected along with foramen magnum decompression. Even after multiple successful neurosurgical interventions, the patient experienced a number of apnoeic episodes requiring intubation and ventilation and a prolonged intensive care unit stay. Despite the exceptionally high frequency and severity of the apnoeic-hypoxic episodes, the patient is demonstrating age-appropriate cognitive development and is now ventilated overnight via tracheostomy. There are lessons to be learnt surrounding the multidisciplinary care of these patients, management of respiratory distress, and the different aetiologies in this case. There was also a correlation found between episodes of urinary tract infection and increased frequency of apnoeic episodes, raising the question of whether her bladder irritation may be partially triggering her autonomic dysreflexia, on a background of a significant surgical history.