We report the application of a three-dimensional skull model with vascular structures for occipital expansion in a patient who had developed occipital emissary veins. A 15-year-old boy visited a dentist for orthodontic treatment and was diagnosed with midface hypoplasia. He had undergone a ventriculo-peritoneal shunt at the age of 10 months. On visiting our institution, he was diagnosed with exophthalmos, low visual acuity, reversed bite, and developmental retardation. Moreover, he had sleep apnea and was supported with continuous positive airway pressure at night. Computed tomography and magnetic resonance imaging demonstrated brachycephalus, chronic tonsillar herniation, midface hypoplasia, and well-developed occipital emissary veins. We chose occipital expansion for lowering intracranial pressure and created a three-dimensional skull model with vascular structures and shunt tube. On this model, we wrote scalp incision and craniotomy lines avoiding injury to the veins and shunt tube. The operation was completed using this plan. Patients with syndromic craniosynostosis frequently have developed emissary veins and previous shunt operation. The three-dimensional skull model with vascular structures will be expected to reduce the risks of surgery.