Background: Non-tuberculous Mycobacteria (NTM) infections are an emerging public health challenge in Indonesia, where overlapping clinical presentations may cause misdiagnosis as tuberculosis (TB), inappropriate treatment, and challenges in TB control. Purpose: To provide the first bibliometric mapping of Indonesian NTM research (2015–2025), assessing productivity, impact, thematic evolution, and research gaps relevant to national diagnostic and surveillance policy. Methods: A systematic search of the Web of Science Core Collection (January 2015–December 2025) combined NTM, atypical mycobacteria, major species, and Indonesia. Following PRISMA-guided screening, 25 primary research articles were analyzed. Total publications (TP), total citations (TC), and H-index were analyzed using VOSviewer (v.1.6.20) and Microsoft Excel to map publication trends, collaboration, and keyword networks. Results: Output increased from fewer than one article annually in 2015–2017, rising from 2018 and peaking at seven articles in 2023, reflecting increased focus on molecular identification. International Journal of Mycobacteriology was the most prolific journal, while Scientific Reports and BMC Microbiology had the highest citation impact (ACP 21 and 9.5, respectively). Japan dominated international collaboration, while Universitas Airlangga led domestic contributions. Five thematic clusters emerged: TB-related infections and assay sensitivity; sputum-based molecular assays; NTM species and susceptibility; diagnosis and disease differentiation; and pulmonary TB with Mycobacterium avium complex features. Conclusion: Indonesian NTM research is shifting toward advanced diagnostics and resistance monitoring, yet remains dependent on international collaboration, underscoring the need for a National NTM Research Consortium to harmonize diagnostic standards and strengthen domestic research capacity.