Nervus intermedius (NI) arises from the superior salivary nucleus, solitary nucleus, and trigeminal tract. It leaves the pons as 1 to 5 roots and travels between the facial and vestibulocochlear nerves before merging with the facial nerve within the internal auditory canal. The mastoid segment of the facial nerve then gives rise to a sensory branch that supplies the posteroinferior wall of the external auditory meatus and inferior pina. This complex pathway renders the nerve susceptible to various pathologies, leading to NI neuralgia. Here, the authors present an unusual intraoperative finding of an atrophic NI in a patient with refractory NI neuralgia and a history of ipsilateral sudden-onset central facial palsy and microvascular decompression for trigeminal neuralgia. The patient underwent NI sectioning via the previous retrosigmoid window and achieved partial ear pain improvement. The gross size of the NI is compared with a cadaveric specimen through stepwise dissection. This case highlights the potential significance of subtle central ischemic events and subsequent atrophy of NI in the pathogenesis of NI neuralgia, as well as the ongoing need to investigate the therapeutic efficacy of nerve sectioning.