Type II Arnold-Chiari malformation (ACM) is an abnormality in which the cerebellum, pons, and medulla oblongata are displaced downward into the spinal cord. Type II ACM is often complicated by respiratory depression, sleep-disordered breathing, and deglutition disorder as a result of medullary dysfunction and impairment of the lower cranial nerves. Bending and stretching of the neck is restricted, and anesthetic management is problematic in patients with the disorder. We performed dental treatment twice under intravenous sedation in a patient with intellectual disability with type II ACM complicated by hypercapnic respiratory failure. Propofol was used for the first sedation procedure. Repeated bouts of respiratory depression occurred on that occasion, so the airway was managed manually by lifting the jaw. However, aspiration pneumonitis occurred postoperatively. A combination of dexmedetomidine and midazolam was used for sedation on the second occasion, and the intervention was completed uneventfully without any respiratory depression. Our experience with this patient highlights the need for selection of an agent for intravenous sedation that does not require neck extension and has minimal effect on respiration in patients with type II ACM, who are at high risk of respiratory depression and pulmonary aspiration.