Rathke's cleft cyst (RCC) is a congenital, benign, epithelial tumor and mainly occurs in sellar region and occasionally in suprasellar region; ectopic RCC is exceedingly rare. We report an uncommon RCC in cerebellopontine angle (CPA) associated with RCC apoplexy and investigated the possible hypothesis of its origin. A 12-year-old female student was admitted to hospital for 3-month history of vertigo, headache, nausea, and vomiting and aggravated for 1 week. Magnetic resonance imaging (MRI) revealed a space-occupying lesion with short T1 and long T2 signals in the left CPA and an intracystic floating nodule with hypointensity on T1- and T2-weighted imaging. The patient underwent the total tumor removal via the retrosigmoid approach with a good recovery. Primary RCC was confirmed by pathology. Follow-up MRI showed no recurrence 3.5 years after craniotomy. Primary RCC can occur in CPA and present special neuroimaging features associated with RCC apoplexy. We presumed that a mimicking mechanism of ectopic craniopharyngioma in CPA leads to the formation in the present case. Microsurgical resection is the optimal strategy for management. Further research and longer follow-up are helpful to better understanding the pathogenesis and development history of RCC in CPA.