Introduction <p><i>Streptococcus pneumoniae</i> can cause serious invasive pneumococcal disease (IPD), such as pneumonia, meningitis and bactaeremia. Two pneumococcal polysaccharide conjugate vaccines (PCV), the 13-valent PCV13 and 10-valent PHiD-CV, are included in the Philippines’ National Formulary and implemented in the national immunisation programme. Recently, a new 10-valent PCV (PCV10-SII) has received World Health Organization prequalification status. The objective of this study was to assess cost-effectiveness of the two 10-valent PCVs versus no vaccination and the relative cost-effectiveness of the two vaccines.</p> Methods <p>An existing Markov model was adapted to the Philippines context. Health outcomes, including bacteraemia, meningitis, pneumonia, acute otitis media (AOM), sequelae and death, were evaluated over a 5-year horizon without discounting. Quality-adjusted life years (QALYs) and costs were calculated over a lifetime horizon, applying a discount rate of 3.66%. The price of PCV10-SII was assumed to be 20% below the PHiD-CV market price; this price reduction was varied between 5% and 15% in scenario analyses.</p> Results <p>Both vaccination strategies dominated the ‘no vaccination’ strategy, producing more health benefits at lower total costs. The incremental cost-effectiveness ratio of PHiD-CV versus PCV10-SII was 54,553 Philippine pesos (PHPs) per QALY gained in the base case analysis. Vaccination with PHiD-CV was predicted to yield more QALYs compared with PCV10-SII (ΔQALY: 2929) since more cases of meningitis, bactaeremia and AOM were prevented but at higher direct costs due to the vaccine price difference. PHiD-CV would be the dominant option if the price reduction for PCV10-SII was at most 5%.</p> Conclusions <p>Both vaccination strategies are superior to no vaccination, producing more health benefits at lower costs. QALYs gained are higher with PHiD-CV but at higher direct costs. Results are most sensitive to assumptions about PCV10-SII vaccine price.</p>