Rationale: Primary clear cell carcinoma of the lung is a rare condition, and presentation as an endotracheal lesion is even more unusual. In this report, we present a patient with clear cell carcinoma occurring in the trachea, which obstructed the tracheal lumen and lead to the respiratory distress. Patient concerns: A 60-year old female patient was admitted due to a 6-month history of dyspnea with worsening symptoms for 1 month. Chest CT scan revealed a smooth nodular shadow with homogeneous density on the wall of upper trachea. Diagnosis: Bronchoscopy therapy and surgical removal of the tumor were performed. The histopathological diagnosis revealed clear cell carcinoma. Intervention: Surgical removal of the clear cell carcinoma was performed. Outcomes: The patient recovered well after the surgery and is now being followed-up after hospital discharge. Lessons: Bronchoscopy is an essential tool for diagnosis of tracheal clear cell carcinoma. Surgical removal should be performed if possible.