OBJECTIVES: Invasive pneumococcal disease (IPD) has reduced significantly following the introduction of pneumococcal conjugate vaccines (PCVs) into the routine national childhood vaccination schedule in New Zealand. However, children continue to suffer from non-invasive pneumococcal diseases, including pneumonia and acute otitis media (AOM), which constitute a large clinical and economic burden. Recent evidence has demonstrated cross-protection for the pneumococcal non-typable Haemophilus influenzae protein-D conjugate vaccine (PHiD-CV; Synflorix™, GSK Vaccines) against invasive disease caused by pneumococcal serotypes 6A and 19A. This study incorporates this recent evidence to compare the cost-effectiveness of PHiD-CV against PCV13 (Prevenar 13™, Wyeth) in a New Zealand birth-cohort.  METHODS: A static Markov cohort model was developed to compare accumulated cost and health benefits of using a 3+1 schedule for PHiD-CV versus PCV13 for a single birth cohort followed over a lifetime. Estimates for model parameters were obtained from locally available databases and published literature. Incremental costs and quality-adjusted life-years (QALYs) were assessed assuming price-parity. A 2+1 schedule for PHiD-CV was also compared to the 3+1 schedule for PCV13 in a scenario analysis. RESULTS: In the base-case 3+1 scenario, PHiD-CV dominated PCV13 by saving New Zealand dollars (NZD) 0.935M in direct costs and 15.8 QALYs. The estimated impact of PHiD-CV and PCV13 was similar for IPD and all-cause pneumonia, but PHiD-CV was projected to have a greater impact on AOM-related outcomes, including myringotomy procedures performed. Nearly 80% of the prevented AOM-related cases were estimated to be accumulated within the first 48 months. A 2+1 schedule for PHiD-CV would result in a cost-saving of nearly NZD 5 million from a single vaccinated cohort compared to a 3+1 schedule for PCV13. CONCLUSIONS: Compared to PCV13, PHiD-CV is projected to be cost-saving from a healthcare provider perspective, offering similar levels of protection against IPD and all-cause pneumonia and higher levels of protection against AOM-related cases.