Giant cell reparative granuloma (GCRG) is a benign nonneoplastic granulomatous lesion and is rare in the cranial bone. We present a pediatric case of this lesion arising from the condyle and lower clivus. A 9-year-old girl presented with slowly progressive hoarseness and dysphagia. She showed left glossopharyngeal, vagus, and hypoglossal nerve palsy. An osteolytic lesion around the lower clivus and condyle joint was accompanied by deformation of the craniovertebral junction. An endoscopic endonasal approach was used to decompress the cranial nerve and confirm the pathological finding. The lesion around the condyle was not resected to preserve occipito-cervical stability. The residual lesion has been observed carefully for 6 months, and regrowth has not occurred. GCRG is a rare granulomatous lesion in the cranial bone. This case is the first report of a pediatric clival GCRG. Treating pediatric GCRG may be helpful.