We report the case of a 52-year-old woman suffering from breathlessness on exertion. A chest radiograph identified a lesion in the intrathoracic trachea. A tumor 0.4 × 0.5 × 0.7 cm in size causing an approximately 80% reduction in the cross-sectional area of the trachea 3 cm above the carina was removed, and histology showed moderately differentiated squamous cell carcinoma. Intrathoracic resection of the tumor and anastomosis was performed through a right lateral thoracotomy. The final histology examination showed atypical papilloma. Polymerase chain reaction-restriction fragment length polymorphism confirmed human papillomavirus-6b in the tumor. The patient remained well 18 months after surgical intervention without recurrence.