Background <p><i>Mycobacterium shinjukuense</i> is a rare type of non-tuberculous mycobacterium (NTM) first reported in Japan. Reported cases of Mycobacterium shinjukuense pulmonary diseases are rare where hosts exhibited apparent risk factors for NTM infection. No consensus has been made on its treatment regimen.</p> Case presentation <p>We report a case of <i>Mycobacterium shinjukuense </i>pulmonary disease in a previously healthy young woman presented as focal bronchiectasis and nodules. The diagnosis was established with <i>16S</i> rRNA sequencing on bronchoalveolar lavage fluid mycobacterium culture. The patient was successfully treated with a thrice-a-week regimen of azithromycin, isoniazid and rifampicin. Whole-exome sequencing revealed mutations in <i>TNFRSF13B </i>and <i>TLR2</i>.</p> Conclusion <p>The presence of <i>Mycobacterium shinjukuense</i> pulmonary disease was confirmed in China. Macrolide, rifampicin and isoniazid was effective in treatment of <i>Mycobacterium shinjukuense</i> pulmonary disease. Genetic susceptibility to NTM should be considered in young patients without apparent risk factors</p>