Recently, ultra-thin bronchoscopy has made it possible to observe smaller bronchi not visualized using standard techniques. We describe a case of pulmonary mucormycosis with cavitation, diagnosed using an ultra-thin bronchoscope. A 15-year-old girl with acute myeloid leukaemia had taken oral prednisolone, 60 mg/day, for graft versus host disease after haematopoietic stem cell transplantation. She was admitted to our hospital with fever and a large cavitary lesion in the right hilum. Using an ultra-thin bronchoscope, the interior of the cavity in the superior segment of the right lower lobe was observed. The bronchoscopic findings revealed debris adhering to the cavity wall with a small volume of effusion. Cunninghamella bertholletiae was isolated from the effusion specimen obtained using the bronchoscope. Pulmonary mucormycosis (C. bertholletiae) complicating an immunocompromised state was diagnosed. Ultra-thin bronchoscopy is useful to diagnose complex pulmonary infections and more research is needed to verify its clinical indications and utility.