A 58-year-old man presented with right chest pain, anorexia, general malaise, and fever. Chest computed tomography showed a mass lesion with right middle lobe atelectasis. The bronchoscopy showed polypoid lesions with a smooth surface in each right middle lobe bronchial lumen. The histopathology revealed the dense accumulation of histiocyte-like cells with foamy cytoplasm under the bronchial epithelium along with yeast-like fungi stained positively with both Alcian blue and Grocott's stains. Cryptococcus neoformans was cultured from the bronchial washings. We diagnosed the patient with pulmonary cryptococcosis with endobronchial lesions. The fluconazole treatment was changed to liposomal amphotericin-B and flucytosine after the diagnosis of cryptococcal meningitis. The minimum inhibitory concentration of the fungi suggested resistance to fluconazole and flucytosine. The lesion regressed after these treatments.