We present the case of a 55-year-old female with pain recurrence after microvascular decompression for trigeminal neuralgia due to development of an arachnoid cyst. Radioimaging studies were inconclusive for vascular compression but showed evidence of fifth nerve distortion. The patient underwent surgical re-exploration, and a cystic lesion of thickened arachnoid containing cerebrospinal fluid was identified and excised. Postoperatively, the patient obtained pain relief. Arachnoid cyst formation may be a possible reason for pain recurrence after microvascular decompression for trigeminal neuralgia, especially when repeat neuroimaging does not show clear evidence of fifth nerve vascular compression. Direct compression from the cyst or arterial pulsation transmission through the cyst to the nerve may be the cause of recurrence.