We report an extremely rare case of an endodermal cyst of the cranio-cervical junction located dorsally to the brainstem and upper cervical spine in a 27-year-old female presented with occipital headache, vertigo and pain in both shoulders. Neurological examination showed neck stiffness with bilateral XIth nerve palsy. Magnetic resonance imaging revealed a cystic lesion at the cranio-cervical junction and slight compression of the brain stem. The lesion was totally removed through the posterior approach. The histological diagnosis was endodermal cyst. To our knowledge, the only one such case has been reported in the literature.