We report a rare case of giant cell tumor in the atlas. A 50-year-old female presented with severe pain in her right neck and shoulder. The preoperative magnetic resonance images showed a tumor mixed with solid and cystic components in the right side of the atlas. CT scan showed that the anterior and posterior arches of the atlas were destroyed. Preoperative biopsy led to the pathological diagnosis of giant cell tumor with multinuclear giant cells and mononuclear stromal cells. A preoperative vertebral angiogram demonstrated tumor stain supplied from the muscular branches. To reduce intraoperative bleeding, the embolization of the right vertebral artery by GDC was performed before surgical removal. The tumor was subtotally removed following ligation of the right external carotid artery to reduce bleeding of tumor. We used the Olerud cervical system to prevent cervical instability after resection of the tumor. Although the symptoms disappeared completely after surgery, regrowth of tumor was observed in follow-up MRI 4 months after the operation. For this reason, local radiation therapy was performed (50 Gy). Then, the size of the tumor has not changed in the 1.5 years since the operation.