Bone xanthoma is an extremely rare and benign tumor in terms of its nature and growth over time. We describe the first case coexisting with ventriculomegaly secondary to aqueduct stenosis (non-tumoral hydrocephalus), the second xanthoma of the clivus described to date. The patient was a 51-year-old woman with headaches and absence seizures. Axial T1-weighted MRI showed a well-demarcated, hypointense, osteolytic, 25 × 18 × 15 mm lesion with cortical erosion located at the right margin of the clivus. Sagittal T2-weighted MRI demonstrated a hypointense mass without associated edema. Sagittal gadolinium-enhanced T1-weighted MRI showed contrast uptake with a partially hypointense rim. The increased ventricular size without periventricular edema was associated with aqueduct stenosis, and there was no contiguity with the tumor. A neuronavigation image-guided transsphenoidal approach was chosen to perform a macroscopically complete resection. Intraoperative histopathological study showed a chordoma of the clivus. Exhaustive postsurgical study revealed the benign nature of a bone xanthoma. Given the finding of a clival lesion, the differential diagnosis is essentially with other malignant entities with a rapidly fatal outcome, such as metastases, or with a possible invasive evolution, such as clivus chordomas. This report describes the clinical, radiological, and pathological keys for such differentiation in order to avoid unnecessarily aggressive treatment with ablative surgery and radiotherapy.