Tuberculosis disproportionately affects low- and middle-income countries (LMICs), where gold standard molecular diagnostic assays like Xpert MTB/RIF are relatively frequently inaccessible. A novel rapid molecular diagnostic test (nLRDT), which can test tongue swab samples, and is more suitable for decentralised primary healthcare settings, has been developed and is currently undergoing preclinical validation. This study evaluated the early cost-effectiveness of this nLRDT vs. Xpert MTB/RIF for diagnosing pulmonary tuberculosis in rural Philippine primary healthcare settings. A hybrid decision tree and Markov model-based cost-effectiveness analysis was conducted from health provider and societal perspectives. Parameters were taken from relevant literature, national-level data, and expert opinion. Costs were expressed in 2024 US dollars and cost-effectiveness evaluated by comparing incremental cost-effectiveness ratios with willingness-to-pay threshold estimates. An estimated willingness-to-pay (WTP) threshold of $1,357 per quality-adjusted life year (QALY) was used. The nLRDT was cost-effective with sputum samples, from both perspectives, with net monetary benefits (NMBs) of $26.62 (societal perspective) and $19.21 (provider perspective) at the WTP threshold of $1,357. Similarly, the nLRDT was estimated to be cost-effective for tongue swab samples from both perspectives, with NMBs of $43.81 (societal) and $24.79 (provider). Sensitivity and scenario analyses identified the specificity of nLRDT as the key driver of cost-effectiveness, with cost-effectiveness maintained at greater WTP thresholds and varying combinations of test performance characteristics. Our findings suggest the nLRDT can be a cost-effective diagnostic tool in rural Philippines, and possibly other similar, contexts. This has positive research, industry, and policymaking implications.