Intraoperative ultrasound (IOUS) serves as a basic imaging tool in neurosurgery. However, its low quality and difficulty in interpreting the images make its use as a resection control tool and navigation system cumbersome. We present our experience using a high-resolution 3D IOUS system combined with a navigation system in pediatric cranial surgery. We retrospectively reviewed 16 pediatric neurosurgical procedures in which a high-resolution 3D IOUS combined with a navigation system was used. The system enables basic navigation based on preoperative computed tomography or magnetic resonance imaging scans. In addition, IOUS images serve as a data set for updated intraoperative navigation. The indications for IOUS were preoperative navigation to define the skin incision and exact craniotomy site, and for real-time neuronavigation and resection control during tumor removal. The added time per case was short and no technical difficulties were encountered. High-resolution 3D IOUS combined with navigation systems has advantages for the pediatric neurosurgical population, including both real-time basic navigation and improved resection control.