A 43-year-old man was referred to our hospital because of an abnormal shadow in his chest radiograph. A chest CT revealed a cavitary lesion in the right upper lung. His sputum and bronchial lavage were negative for acid-fast bacilli and tuberculosis (TB)-polymerase chain reaction (PCR). However, a gastric juice smear was positive for acid-fast bacilli, and Mycobacterium xenopi was cultured eight weeks later. He started taking antimycobacterial drugs. Although he had been treated for six months, CT findings showed but minimal improvement. He underwent a partial right-upper lobectomy, since the lesion was a solitary nodule without satellite, and M. xenopi had been cultured only once from gastric juice. Excised tissue was positive for acid-fast bacilli, and M. xenopi was isolated despite his six-month treatment. We find that a surgical resection is recommended if the lesion is limited. In Japan, pulmonary infections with M. xenopi are rare, but in the future, the number of cases will increase with the development of better diagnostic techniques. It is necessary to establish a treatment paradigm for M. xenopi.