Tuberculosis (TB) remains a serious public health challenge despite enormous eradication efforts. Indigenous groups worldwide have a higher TB incidence and associated delayed sputum-smear conversion. The aim of this case-control study was to determine the epidemiology and factors associated with delayed sputum-smear conversion among Malaysian aborigines. We used secondary data from 2016 to 2020 in the MyTB surveillance system. Malaysian aborigines with smear-positive pulmonary TB were enrolled and followed until the end of the intensive phase. Descriptive statistics and multiple logistic regression were used for data analysis. Of 725 Malaysian aborigines with pulmonary TB, 572 (78.9%) were smear-positive and 487 (78.9%) fulfilled the study criteria. The mean (SD) age of smear-positive pulmonary TB was 39.20 (16.33) years. Majority of participants were male (63%), Senoi tribe (54.9%), living in rural areas (88.1%), formally educated (60.4%) and living below the poverty line (97.1%). Overall, 93 (19.1%) of 487 patients showed delayed sputum-smear conversion and significantly associated factors, such as smoking (AdjOR: 3.25; 95% CI: 1.88, 5.59), diabetes mellitus (AdjOR: 12.84; 95% CI: 6.33, 26.06), and HIV infection (AdjOR: 9.76; 95% CI: 3.01, 31.65). Stakeholders should adopt targeted approaches to tackle the problem of aboriginal groups with pulmonary TB and these associated risk factors to realise the End TB target.