Clear cell meningioma (CCM) is a WHO classification Grade II meningioma. It is a very rare disease, of which only 41 cases of spinal cord CCM in children have been reported to date. CCMs sometimes do not have the "dural attachment" that is usually found in meningiomas, and our understanding of the origin of CCMs is therefore controversial. We hereby present a case of pediatric CCM of the lumbar spine, in which we examined intraoperatively, the detailed anatomical location of the tumor. The case is a 10-year-old boy, who presented to our hospital with a 2-month history of lower back and bilateral lower extremity pain upon waking, which gradually worsened. Lumbar spine CT and MRI revealed an intradural extramedullary tumor at the L3 vertebral level, and surgery was performed to remove it. The tumor was in close contact with the dura mater, and also in contact with the cauda equina via the arachnoid. The tumor was likely located primarily between the dura mater and arachnoid. The pathological diagnosis was CCM, with an MIB-1 index of less than 1%. His back pain and bilateral lower extremity pain improved after surgery, and he was discharged from our hospital. Postoperative radiation therapy was not performed. Based on this case, we suggest that intraoperative examination of the anatomical location of these tumors and accumulation of relevant experience are important to elucidate the embryological mechanisms of this rare disease.