Bacillus Calmette-Guerin (BCG), the only available vaccine for tuberculosis (TB), has been applied for decades. The Indonesian government recently introduced a national TB disease control programme that includes several action plans, notably enhanced vaccination coverage, which can be strengthened through underpinning its favourable cost-effectiveness. We designed a Markov model to assess the cost-effectiveness of Indonesia's current BCG vaccination programme. Incremental cost-effectiveness ratios (ICERs) were evaluated from the perspectives of both society and healthcare. The robustness of the analysis was confirmed through univariate and probabilistic sensitivity analysis (PSA). Using epidemiological data compiled for Indonesia, BCG vaccination at a price US$14 was estimated to be a cost-effective strategy in controlling TB disease. From societal and healthcare perspectives, ICERs were US$104 and US$112 per quality-adjusted life years (QALYs), respectively. The results were robust for variations of most variables in the univariate analysis. Notably, the vaccine's effectiveness regarding disease protection, vaccination costs, and case detection rates were key drivers for cost-effectiveness. The PSA results indicated that vaccination was cost-effective even at US$175 threshold in 95% of cases, approximating the monthly GDP per capita. Our findings suggest that this strategy was highly cost-effective and merits prioritization and extension within the national TB programme. Our results may be relevant for other high endemic low- and middle-income countries.