The authors present the case of a 2-year-old boy with bobble-head doll syndrome (BHDS) associated with a large suprasellar arachnoid cyst and enlarged ventricles, who was successfully treated with neuronavigated laser-assisted endoscopic ventriculocystocisternostomy. The clinical history, surgical treatment, and clinical follow up of the patient are described. A navigated laser-assisted endoscopic ventriculocystocisternostomy of the suprasellar arachnoid cyst led to cessation of the head bobbing, and notable reduction of the cyst and ventricles was visible on the postoperative magnetic resonance images. Caused by a suprasellar arachnoid cyst, BHDS can be successfully treated with navigated laser-assisted endoscopic ventriculocystocisternostomy. The advantages of this procedure are minimal invasiveness and facilitated guidance of the neuronavigation system to the target area when normal anatomical landmarks are not visible.