Introduction. Synovial cysts rarely develop in the atlantoaxial joint. We report a case of posterior C1-2 laminectomy for a synovial cyst of the atlantoaxial joint which passed through the dorsal dura and put pressure on the cervical spinal cord. Case Presentation. A 62-year-old man with rapid progression of pain and weakness in the left upper extremity presented to our hospital. A cervical spine X-ray showed left C5-6 and C6-7 stenoses. A cervical magnetic resonance imaging showed an intradural extramedullary cystic lesion on the right side of the ventral cervical spinal cord at the C1-2 level and severe compression of the cervical spinal cord. Because a cyst was partially enhancing, a tumor lesion was not identifiable. Due to severe spinal cord compression, we performed intradural cyst removal via a posterior intradural approach with C1-2 laminectomy and left-sided C5-6 and C6-7 foraminotomies. One year after surgery, the cyst did not recur, and atlantoaxial instability did not appear. Discussion. A compressive lesion on the cervical spinal cord was not identified preoperatively as a synovial cyst. However, intraoperative and pathological findings suggested that the compressive lesion can be a synovial cyst which passed through the dorsal dura. The surgical treatment strategy for a synovial cyst of the atlantoaxial joint is controversial due to factors, such as the presence of atlantoaxial instability, level of cyst causing compression of the cervical spinal cord, severity of myelopathy, and cyst location. In the present study, the cervical spinal cord was highly compressed and the cyst was located on the right side of the cervical spinal cord; we chose cyst removal through a posterior intradural approach with C1-2 laminectomy.