Atlantoaxial synovial cysts can very rarely penetrate the dura mater into the thecal sac and cause direct neural compression. Several case reports have been available on "intradural synovial cysts" (IDSCs). In this study, we report on a case with an atlantoaxial IDSC mimicking an extradural lesion. A 90-year-old man was diagnosed with a cystic lesion located laterally to the atlantoaxial joint adjacent to the retro-odontoid pseudotumor (ROP) causing cervical spinal cord compression. Thus, surgical removal was planned. On preoperative examination, the cyst, which had a two-layer structure showing a T2-isointense small mass inside a T2-hyperintense lesion, was thought to be located in the extradural region. However, operative findings showed that the cyst was located inside the dura mater. Histopathological examination suggested a synovial cyst. No recurrence of the cyst was observed until the latest follow-up after 3 years, and the ROP decreased in size. Almost all IDSCs reported previously were observed in the medial site of the atlantoaxial joint. In our case, however, the cyst was observed adjacent to the posteromedial site of the right atlantoaxial joint and the ROP, mimicking an extradural lesion. We had no knowledge regarding the IDSC before the surgery and assumed an extradural lesion. Albeit rare, the existence of such a condition should be considered.