BACKGROUND: Gangliogliomas are low-grade gliomas typically found in the temporal lobes with a low rate of malignant transformation. In rare cases, they may be found in the spinal axis. OBSERVATIONS: An 8-year-old boy presented with 2 months of neck pain and upper extremity incoordination and was found to have a cervicomedullary lesion. An occipital craniectomy and a C1 laminectomy with C2-5 laminoplasty were performed for biopsy and partial resection. The pathological diagnosis was consistent with ganglioglioma, and the patient was followed with serial MRI. He presented 1.5 years later with urinary incontinence and a precipitous decline in upper extremity strength. MRI showed expansion of the cervicomedullary junction with new ring enhancement. A repeat biopsy was performed, showing glioblastoma. The patient underwent daily radiotherapy, with improvement in his upper extremity weakness. Subsequently, the patient was started on chemotherapy and required placement of an external drain followed by a programmable ventriculoperitoneal shunt prior to his unfortunate death. LESSONS: In this case, the ganglioglioma arose in the cervical spine, with malignant transformation to glioblastoma 1.5 years after diagnosis. In children with a history of spinal ganglioglioma presenting with bowel/bladder dysfunction and worsening strength, a differential diagnosis of malignant progression should be kept in mind. https://thejns.org/doi/10.3171/CASE24442.