Purely intradural retro-odontoid synovial cysts are rarely reported in neurosurgical literature, particularly in the absence of associated bony erosions. We present the case of a 57-year-old Native American male with a retro-odontoid synovial cyst and a history of chronic refractory neck pain that was adequately decompressed via an endoscopic-assisted far-lateral approach using a C1-2 hemilaminectomy, obviating the vertebral artery (VA) transposition, bony instability, and the need for instrumented bony fusion. The patient presented to our clinic with several months of refractory nuchal and cervical spine pain and crepitation affecting his activities of daily living (ADL). MRI findings revealed an intradural cyst at the level of C2 behind the odontoid process impinging on the medulla and causing early VA displacement. Both stereotactic neuro-navigation and microsurgical visualization aided in the manipulation of the endoscope and attaining the caudocranial working trajectory. The patient remained neurologically non-lateralizing postoperatively, similar to his preoperative status. This article highlights a less invasive surgical exposure with an endoscope-assisted caudocranial trajectory obtained by a limited unilateral hemilaminectomy to achieve the desired outcome.