Background: Preventing mother-to-child transmission of human immunodeficiency virus is important due to the impact of the disease to the women and their children’s health. Established guidelines have recommended strengthening the ability to detect and treat HIV as early as possible. This study attempts to explore cost-effective PMTCT interventions in a low incidence, low-middle income setting such as the Philippines that can be replicated in other similar country settings.Methods: The study utilized a model-based cost-effectiveness analysis through a decision tree analysis. The decision tree reflected the first ANC visit of a pregnant woman in the Philippines. Vertical transmission program was explored as ten possible PMTCT policy strategies including Do-nothing approach; status quo approach, which had 9% HIV testing, provision of tenofovir-based ART and neonatal prophylaxis, and automatic cesarean section; Eight universal screening policy strategies, which had 100% HIV testing and counselling, provision of tenofovir-based ART and neonatal prophylaxis with inclusion or exclusion of raltegravir for aggressive late antenatal care (ANC) HIV treatment on top of the ART given, breastfeeding or provision of substitute feeding, and normal delivery or cesarean section deliveryResults: Base case analysis revealed that policy strategy of universal HIV screening, with additional provision of raltegravir on those receiving late antiretroviral therapy, neonatal prophylaxis, and substitute feeding on normal delivery (urndnpsf) had the lowest ICER values among all policy strategies compared to status quo (₱291,170.26/QALY) and do nothing (₱291,710.26/QALY). Through universal screening coverage, at least 91% of the HIV cases in newborn may be averted. Cost of HIV test must be reduced by at least 45% to have a cost-effective PMTCT program. Alternatively, by performing group pre-test HIV counselling of at least three persons per session, the program will become cost-effective when compared to the unofficial Philippine threshold of ₱150,000/QALY.Conclusions: Model design on HIV testing among pregnant women allows exploration of costs and outcomes of PMTCT interventions that focused on a low prevalence, low-middle income setting. From the study, HIV testing can be a major cost constraint for PMTCT. Furthermore, by performing group pre-test HIV counselling instead of per individual, a cost-effective PMTCT program may be achieved.