Neuronavigation systems have been developed for image-guided neurosurgery to aid in the accurate resection of malignant brain tumors. Therefore, the accuracy of the neuronavigation is important. However, many factors can reduce the navigation accuracy during surgery. Before craniotomy, the patient's head is secured to a head frame with head pins; this fixation may cause displacement of fiducial markers and reduce the accuracy. We term this phenomenon skin shift. In this study, the extent of skin shift and its effect on navigation accuracy were determined by use of both preoperative magnetic resonance imaging (MRI) scans acquired before fixation and intraoperative MRI scans acquired after fixation. We measured the displacement of the fiducial markers by using fusion images obtained by integrating preoperative and intraoperative MRI scans. We also evaluated the navigation accuracy of registration based on preoperative and on intraoperative MRI. The mean (± SD) extent of skin shift was 5.34 (± 2.65) mm. The navigation accuracy of registration based on preoperative MRI was 4.06 (± 2.25) mm, and that of registration based on intraoperative MRI was 2.51 (± 1.32) mm. No significant correlation was observed between the extent of skin shift and the distance between the head pins and fiducial markers (p > 0.05). The navigation accuracy of registration based on intraoperative MRI was significantly higher than that of registration based on preoperative MRI (p < 0.001). The results indicated that skin shift was caused by the fixation, and that this shift reduced the navigation accuracy. Intraoperative MRI can correct the effect of skin shift.