A 68-year-old woman was found to have an abnormal shadow on chest X-ray. Computed tomography showed some small ground-glass opacities in the bilateral lung field and also a 22-mm tumor in the left lower lobe, which showed high accumulation on (18)F fluorodeoxyglucose positron emission tomography. Each of them was difficult to distinguish from lung cancer clinically. Preoperative localization of a small ground-glass opacity nodule with computed tomography-guided lipiodol marking and resection of each using a fluoroscopic unit was performed. Pathological findings from the small nodule showed minute pulmonary meningothelial-like nodule, and those from the tumor and fungal culture showed pulmonary cryptococcosis. To the best of our knowledge, this is the first reported case of coexisting minute pulmonary meningothelial-like nodules and pulmonary cryptococcosis mimicking lung cancer. Thoracoscopy assisted by computed tomography-guided lipiodol marking enabled us to diagnose them.