There are various causes of ventriculoperitoneal shunt (VPS) failures. Patients who receive shunt placement during childhood need follow-up for decades as they grow, especially in the early periods of life. Herein, we report a rare case of mechanical shunt obstruction in a pediatric patient in whom a cramped burr hole and skull growth compressed the tube and obstructed cerebrospinal fluid flow. A 6-year-old girl presented to our hospital with nausea and headache. She was born preterm and developed intraventricular hemorrhage followed by VPS placement for hydrocephalus; thereafter, she had no need for shunt revision until this admission. After careful evaluation of the patency of the shunt system, the presence of tube stenosis was suspected at the site of the shunt tube penetrating the burr hole of the skull. During the operation to revise the shunt tube, a compressed tube was observed at the exit from the skull. After enlarging the narrowed burr hole and reconstructing the proximal catheter, her symptoms immediately improved. Previously, only one case of shunt malfunction due to tube compression from bone growth has been reported in a pediatric patient with osteopetrosis. To the best of our knowledge, such a condition has never been described in pediatric patients with no metabolic bone disease. Although it is rare, obstruction at the exit from the skull due to bone growth should be included in differential diagnoses for young patients during a long follow-up after VPS.