Fluid-filled cavities within the brain are well-recognized in human and veterinary medicine. Congenital or acquired brain cystic lesions could be isolated or associated with other diseases. Clinical signs related to cysts depend on their size and the mass effect they exert on surrounding neuroanatomical structures. We present a case of a 5-month-old Belgian Malinois dog with cervical pain and right head tilt. The dog had a normal haematochemical profile and negative infectious disease tests. A contrast enhancement Computed Tomography scan revealed the presence of a thin-walled cystic lesion in the caudal cranial fossa at the level of the right pontine-cerebellar junction. A cerebrospinal fluid tap was performed by lumbar puncture, revealing a monocytic pleocytosis. After initial improvement following corticosteroid and antibiotic therapy, clinical signs worsened, and the dog underwent a second clinical evaluation and magnetic resonance imaging examination. After euthanasia a complete postmortem examination was performed. Histological and immunohistochemical findings were suggestive of an ependymal cyst.