Background Microvascular decompression (MVD) is known as a safe and effective procedure to treat glossopharyngeal neuralgia (GN). However, some patients experienced poor pain relief after MVD, for which the mechanism is not clear yet. Reviewing the intraoperative findings and postoperative effect of reoperation for patients who failed the first MVD, is helpful to figure out why the first MVD for GN failed. Methods There were eight patients with GN who failed first MVD. The possibilities for secondary GN were eliminated by physical and radiological examination. The reoperation through the previous incision was conducted, and appropriately, treatment was provided according to the intraoperative findings. The video data and prognosis of the reoperation were retrospectively reviewed. The reasons for the invalid first MVD were analyzed. Results To the end of follow-up, there were 7 patients of pain-free, and one patient with occasional mild pain attacks (VAS 2). There was one patient who experienced transient hoarseness in 3 months after the reoperation. We summarized the causes for failed first MVD which were omission of the offending vessel in 3 cases, inadequate decompression of the nerve root in 2 cases, and excessive decompression materials which caused iatrogenic nerve root compression in 3 cases. Conclusions For patients with recurrent or failed after MVD, a thorough examination should be carried out to eliminate the possibility of secondary GN. Reoperation through the previous incision is safe and effective. The bone window should be close enough to the sigmoid sinus to aid the exposure of the nerve root. The nerve transection could be adopted if no offending vessels were found. And a multi-site decompression could be used when the vertebral artery is the offending vessel.