Purpose To report a rare case of tibial osteomyelitis caused by Mycobacterium aubagnense and its L-form, to systematically review non-tuberculous mycobacteria (NTM) infections of the bones, and to summarize the medication guidelines for infections with NTM and its L-forms. Methods Case report and literature review. Results We report a 31-year-old HIV-positive man who developed osteomyelitis caused by M. aubagnense and its L-form. Culture, electron microscopy, polymerase chain reaction assay, and a reversion test confirmed the existence of M. aubagnense . The patient was treated with surgical debridement and a combination of systemic antibiotics, and continued to take antiretroviral treatment. Some clinical improvement was noted shortly after the initiation of this treatment. Resolution of osteomyelitis was achieved after 10 months. We also systematically reviewed cases of NTM osteomyelitis in the PubMed database and compared antibiotic sensitivity between L-forms and their prototype bacteria. We have summarized the treatment regimens for infections of the bone and bone marrow caused by NTM and their L-forms. Conclusion We have reported the first case of refractory osteomyelitis caused by M. aubagnense and its L-form in a patient with immune deficiency, reviewed the literature on NTM osteomyelitis, and compared the antibiotic sensitivity of L-forms and their prototype bacteria.