A 44-year-old woman underwent a follow-up examination for Crohn's disease 9 years ago. Chest computed tomography (CT) showed an infiltration shadow with a cavity in the right upper lobe. After a CT-guided lung biopsy, epitheloid granuloma was noted, and an acid-fast bacilli examination was smear-positive, but a culture examination was negative. Because the abnormal chest shadow with cavity gradually increased and right shoulder pain appeared, we performed bronchoscopy again six months later. Mycobacterium heckeshornense was isolated from the bronchoalveolar lavage fluid specimen, so we diagnosed her with pulmonary M. heckeshornense disease. Isoniazid, rifampicin, and ethambutol were administered, and the abnormal chest shadow improved.