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Background: Glossopharyngeal neuralgia is a rare but severe and disabling pain condition often caused by vascular compression of the glossopharyngeal nerve. Treatment is similar to that of trigeminal neuralgia, but some patients may be refractory to both medical and surgical approaches. Here we present a case of refractory glossopharyngeal neuralgia that responded well to onabotulinumtoxinA (BTX‐A). Case: We report a case of a 65‐year‐old man with well‐controlled human immunodeficiency virus disease with glossopharyngeal neuralgia symptoms since 2015. He had partial response to medications but was limited by side‐effects. He underwent microvascular decompression twice with initial relief both times, but experienced recurrence of attacks 1–3 years after each surgery. He was treated with BTX‐A using the chronic migraine PREEMPT protocol (i.e., 31–39 injection sites in head and neck muscles), which led to significant relief of his glossopharyngeal neuralgia pain. Conclusions: This is the first case to our knowledge of glossopharyngeal neuralgia treated with BTX‐A. BTX‐A can be an effective treatment for glossopharyngeal neuralgia, even when injections are not administered directly over the sensory distribution of the glossopharyngeal nerve. [ABSTRACT FROM AUTHOR]