We have used MRI-based three-dimensional (3D) reconstruction and a real-time, frameless, stereotactic navigation device to facilitate the removal of seizure foci in children suffering from intractable epilepsy. Using this system, the location of subdural grid and strip electrodes is recorded on the 3D model to facilitate focus localization and resection. Ten operations were performed, including 2 girls and 8 boys ranging in age from 3 to 17, during which 3D reconstruction and surgical instrument tracking navigation was used. In all the cases, the patients tolerated the procedure well and showed no postoperative neurological deficits. We believe this to be a valuable tool for a complete and safe resection of seizure foci, thereby reducing the incidence of postoperative neurological deficits and significantly improving the overall quality of life of the patients.