We have applied the neuronavigation system to endoscopic biopsy and third ventriculostomy in the management of patients with a pineal tumor with hydrocephalus. With the guidance of neuronavigation, the two optimal sites of burr hole and trajectories were planned preoperatively, and the advancing endoscopic device was monitored in real time during the procedure. In our five patients, the diameters of the tumors were 2-3 cm, and the mean systemic accuracy of registration with neuronavigation was 1.2 mm. The biopsy and third ventriculostomy were performed successfully via the respective optimal burr hole and the trajectory determined using preoperative neuronavigation. There were no procedure-related complications, and none of the patients needed another procedure for CSF diversion during the follow-up periods. We present our technique which includes the application of the neuronavigation system to the biopsy and third ventriculostomy in pineal tumor with associated hydrocephalus. This technique can be performed using a simple rigid endoscope via the determined optimal entries and trajectories. The optimal preoperative planning and the intraoperative guidance by neuronavigation are thought to be able to give more chances to minimize the brain injury related to movements or deviation of endoscopic device.