Differential diagnosis of stylalgia is broad, and many causes should be taken into account, such as temporomandibular joint disorders, carotidynia, compression of nerve fibers by neoplasms, cranial nerve neuralgias, chronic pharyngotonsillitis, pharyngeal or base of tongue tumors and elongation of styloid process, or Eagle syndrome. Basicranium malformation can determine a rare form of stylalgia that is caused by dislocation of styloid process. This can produce a reduction of maxillo-vertebropharyngeal space and irritation of nerve fibers together with stylopharyngeal muscular chronic contraction. This case report illustrates the diagnostic dilemma and surgical strategy experienced in a rare case of stylalgia caused by a dislocation of styloid process produced by a basicranium malformation. Basicranium malformation should be considered in the pathogenesis of stylalgia when a styloid process with normal dimension is encountered.