Intramedullary spinal cord tumors are rare in children. Regardless of the type of tumor, surgical removal is thought to improve progression-free survival. However, postoperative kyphosis is a serious problem in children, who can expect long-term survival. We present a pediatric case of neurofibromatosis type 2-related spinal ependymoma at the cervicothoracic regions where acute neurological deterioration was developed due to a combination of tumor recurrence and postoperative kyphotic deformity. In the first surgery, subtotal tumor resection was performed via osteoplastic laminotomy. Postoperative radiological evaluation at several months showed cervicothoracic junctional kyphosis, which subsequently made a significant improvement by lifestyle instructions. However, 22 months after the surgery, he exhibited rapid neurological deterioration caused by the regrowth of the recurrent tumor and re-emergence of kyphotic deformity, which led to the fixed laminar flap sank into the spinal canal. Therefore, a second surgery was performed 23 months after the first surgery, and gross total removal was achieved. Osteoplastic laminotomy is presumed to reduce the occurrence of postoperative kyphosis compared with laminectomy, but there have been no reports on the spinal cord compression by plunging of the re-fixed laminar flap into the spinal canal. The kyphosis deformity increases the chance of re-fixed laminar flap coming off, thereby accelerating neurological injury on top of the neural damage by tumor recurrence itself. Therefore, pediatric patients with spinal cord tumors should be carefully managed in terms of recurrent tumors and postoperative kyphosis, and timely surgical intervention is necessary before kyphotic deformity becomes evident.