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Introduction: Giant cell tumor of bone (GCTB) is a rare, typically benign neoplasm that primarily affects long bones in adults, with clival involvement being extremely rare, particularly in pediatric cases: a mini-review shows a total of 28 described cases, of which only 5 were truly pediatric (within 14 years of age). Surgery is the treatment of choice, and Denosumab is reported to be the most effective drug therapy. To date, the GCTB’s molecular hallmark is the somatic mutation p.Gly34Trp, at the H3F3A gene (H3.3 p.Gly34Trp mutation), but in this case, the mutation H3.3 p.Gly35Trp was identified. Case Presentation: A 9-year-old female presented with progressive ocular pain, ptosis, and diplopia. MRI revealed a 42 × 32 × 30 mm mass in the clivus and sphenoid body. The patient underwent partial resection, and histology confirmed GCTB. Molecular testing revealed the presence of the H3.3 p.Gly35Trp mutation, and we demonstrate that this is the true mutation associated with GCTB, not the previously described (H3.3 p.Gly34Trp). Due to residual tumor tissue, the patient was treated with Denosumab, a RANKL inhibitor. During a 2-year follow-up, the tumor size stabilized, and no significant adverse effects were observed. Conclusion: This case represents the first pediatric clival GCTB harboring the H3.3 p.Gly35Trp mutation. Molecular diagnostics played a crucial role in confirming the diagnosis and demonstrating that the true mutation harbored by GCTB is H3.3 p.Gly35Trp and not the formerly described (H3.3 p.Gly34Trp). Denosumab therapy effectively controlled the tumor without major side effects, although long-term treatment duration and safety require further study.