The insertion of ventriculoatrial (VA) shunts for the treatment of hydrocephalus is associated with the development of chronic thromboembolic pulmonary hypertension (CTEPH). Chronic thromboembolic pulmonary hypertension occurs in patients with recurrent or chronic pulmonary embolism, and is a rare but, potentially devastating disease in children. Pulmonary thromboendarterectomy (PTE) is an important curative therapy for patients with CTEPH. Herein, we present a case of a 14 year-old male patient with CTEPH that developed after a VA shunt procedure. After successful PTE, systolic pulmonary artery pressure was decreased from 75 mmHg to 30 mmHg. PTE is recommended in the pediatric CTEPH population.