OBJECTIVES: The objective of this study is to evaluate the costs-effectiveness of introducing pneumococcal conjugate vaccine as part of the childhood immunization program in the Philippines. METHODS: A cost-utility analysis was conducted using a lifetime horizon. A Markov simulation model was used to examine the comparative cost-effectiveness of PCV10 and PCV13 against the current scenario of no vaccination. A health system perspective was employed to explore different funding schemes, which include full or partial vaccination coverage subsidized by the government and self-paid vaccination in the private sector.  An annual discount rate of 3.5% for future costs and outcomes was applied. Results were presented as incremental cost-effectiveness ratios (ICERs) per QALY gained. Sensitivity analysis was performed to determine the impact of parameter uncertainty. RESULTS: With universal vaccination by the government at a cost per dose of Php 624 for PCV10 and Php700 for PCV13, the ICER for PCV10 and PCV13 were Php 68,086 and Php 67,631 per QALY gained, respectively, compared to no vaccination. Partial vaccination of 25% and 50% of the birth cohort yielded considerably higher ICER values that are still below the country ceiling threshold of Php 170,000 per QALY gained, because of the loss of herd protection. The analysis also found that with a partial vaccination strategy of the government, having at least 10% of the target cohort self-pay a higher market price of Php 2.056 for PCV10 and Php 3,545 for PCV13 would make vaccination cost-ineffective, because of the high out-of-pocket costs.  CONCLUSIONS: The inclusion of PCV in the national immunization program with either universal or partial coverage would be a cost-effective intervention in the Philippines compared to no vaccination. However, the affordability and sustainability of PCV implementation over the long term should be considered by decision makers.