Jugular foramen syndrome (JFS) results from a dysfunction of the lower cranial nerves (CN IX–XII) traversing the jugular foramen and presents with diverse clinical manifestations depending on the nerves involved. Surgical resection is the primary treatment for benign jugular foramen tumors, but postoperative neurological deterioration remains a significant concern. This paper reports a case of worsened dysphagia following the surgical treatment of JFS despite anatomical preservation of the lower cranial nerves. A 68-year-old man presented with long-standing left-sided hearing loss, tongue atrophy, and a recent onset of dysphagia. Imaging revealed a left jugular foramen mass that was initially suspected of being a schwannoma. The patient underwent tumor removal via a combined transcochlear and transcervical approach, with intraoperative preservation of CN IX–XII. Histopathology confirmed paraganglioma. Postoperatively, the patient experienced aggravated dysphagia, with video fluoroscopic swallowing studies showing persistent residue in the left pyriform sinus. Although the subjective swallowing function gradually improved, the neurological deficits did not fully recover. This case shows that even when a preexisting cranial nerve dysfunction is present and the nerves are preserved intraoperatively, the swallowing function can deteriorate after surgery. Therefore, a thorough preoperative functional assessment and careful consideration of potential postoperative functional decline are essential in the surgical management of jugular foramen tumors.