Background Prepontine (suprasellar) arachnoid cysts are uncommon in clinical practice, so experiences in their management are limited and the best method of treatment for them remains unclear. Here we report our experience in using stereotactic cyst/ventricular-peritoneal shunting for the treatment of prepontine arachnoid cyst. Case Description A 42-year-old woman with prepontine arachnoid cyst was treated with cyst/ventricular-peritoneal shunting: the ventricular catheter was precisely inserted at a point where it could drain from the cyst and the ventricle at the same time. The postoperation CT scan showed that the cyst and the enlarged ventricle shrunk markedly. During a 1-year follow-up period, she remained symptom-free and had returned to full-time work. Conclusion Stereotactic cyst/ventricular-peritoneal shunting appears to be an effective method for treating prepontine arachnoid cyst.