Alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome affects males and is associated with profound developmental delay, facial dysmorphism, genital abnormalities, and alpha thalassemia. Appropriate oral health management for affected patients is important. The purposes of this report are to describe a case involving six years of oral health management, including training in eating, drinking and swallowing, for a patient with ATR-X syndrome, and to discuss the morphological and functional oral characteristics of this disorder. The patient's oral dysfunctions were incompetent lip-closing, inappropriate tongue protrusion, deviation of chewing acquisition, and incompetent oral and pharyngeal bolus propulsion. Other problems included inappropriate ingestion posture, low interest in meals, and poor oral hygiene. A stable oral intake and an improved eating posture were achieved through an intervention; however, the patient's inappropriate tongue protrusion, deviation of chewing acquisition, and incompetent bolus propulsion remained unchanged.