Children with severe impairment of the central nervous system (CNS) experience gastrointestinal (GI) symptoms at a high rate and severity, including retching, vomiting, GI tract pain, and feeding intolerance. Commonly recognized sources of symptoms include constipation and gastroesophageal reflux disease. There is growing awareness of sources due to the impaired nervous system, including visceral hyperalgesia due to sensitization of sensory neurons in the enteric nervous system and central neuropathic pain due to alterations in the thalamus. Challenging the management of these symptoms is the lack of tests to confirm alterations in the nervous system as a cause of symptom generation, requiring empirical trials directed at such sources. It is also common to have multiple reasons for the observed symptoms, further challenging management. Recurrent emesis and GI tract pain can often be improved, though in some not completely eliminated. In some, this can progress to intractable feeding intolerance. This comprehensive review provides an evidence-based approach to care, a framework for recurrent symptoms, and language strategies when symptoms remain intractable to available interventions. This summary is intended to balance optimal management with a sensitive palliative care approach to persistent GI symptoms in children with severe impairment of the CNS.