Soft tissue infections with Mycobacterium mageritense are uncommon. We report the case of a 5-year-old girl who developed a subcutaneous abscess in her right ankle caused by M. mageritense. She had a history of acute encephalopathy and adrenal insufficiency and was hospitalized for acute pancreatitis. During hospitalization, the patient developed fever and tachycardia. Blood culture was positive for gram-positive bacilli. Although initial testing with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) reported a different organism, a repeat test identified M. mageritense. One month after the positive blood culture, she developed redness and swelling in the right ankle. The pus from the subcutaneous abscess after drainage grew M. mageritense, which was further confirmed by the sequencing of housekeeping genes. Based on sensitivity testing, the patient was treated with tosufloxacin and linezolid. The local inflammatory signs gradually improved on starting the treatment. The antibiotics were administered for 6 months, and she experienced no relapse during the 8 months of follow-up after the completion of therapy. This is the first case report of a pediatric M. mageritense infection, which also highlights an important potential pitfall of MALDI-TOF MS. Further, we observe that the choice of antimicrobials for the treatment of M. mageritense is more limited in children than in adults.