In a 9-year-old Yorkshire terrier a cyst of the respiratory epithelium of the nasopharynx was diagnosed. A complete obstruction of the nasopharynx leading to dyspnea was detected by computed tomography and endoscopy. A minimally invasive ablation of the cystic wall was performed under endoscopic guidance, followed by a pathohistological examination. Immediately after resection of the cyst, the clinical symptoms resolved. The follow-up endoscopical examination 3 months postoperatively was unremarkable. In the presented case the minimally invasive endoscopic ablation of the cystic wall was a successful treatment method.