A 69-year-old man presented with progressive paralysis of the right arm and leg with a past history of metastatic rectal cancer. Magnetic resonance imaging showed a cystic mass lesion posterior to the odontoid process. Under a preoperative diagnosis of intradural extramedullary tumor, partial transcondylectomy and C1 hemilaminectomy were performed, and the cyst was removed through a transdural approach, decompressing the medulla oblongata and the cervical spinal cord. The histological diagnosis was juxtafacet cyst (ganglion cyst). An atlantoaxial intraspinal juxtafacet cyst at the level of the odontoid process is extremely rare. In our case, the cyst was removed using a posterior approach, resulting in rapid improvement in symptoms.