Background/Objectives: The incidence of nontuberculous mycobacterial (NTM) infections has increased globally; however, the clinical manifestations and optimal treatment strategies for extrapulmonary NTM infections remain poorly defined. This study assessed the clinical manifestations and treatment outcomes of extrapulmonary NTM infections. Methods: Data from adult patients with suspected extrapulmonary NTM infections at a tertiary-care hospital from 2009–2022 were categorized into NTM disease and isolation groups. Diagnosis of NTM disease relied on stringent criteria, whereas isolation required NTM isolation without meeting the criteria for infection. Results: Among 75 patients evaluated, 32 (42%) were diagnosed with NTM disease and 43 (57%) with NTM isolation. History of immunosuppressant use within the past 3 months (p = 0.070) and injection (p = 0.001) were more frequent in the disease group. The median interval from symptom onset to evaluation was 106.6 and 20 days in the disease and isolation groups, respectively. The prevalence of positive NTM polymerase chain reaction results (36.4%, p = 0.003) and acid-fast bacillus staining (39.1%, p < 0.001) was significantly higher in the disease group than in the isolation group. Mycobacterium intracellulare (21.9%), M. abscessus (15.6%), M. chelonae (9.4%), and M. fortuitum complex (9.4%) were the most frequently identified species. Of the 27 patients in the disease group who received treatment, 13 improved, four experienced treatment failure, seven were lost to follow-up, and three died during treatment, with one death directly attributable to NTM disease. Conclusions: NTM disease exhibits a spectrum of clinical manifestations. Accurate diagnosis is crucial for initiating effective treatment.