ABSTRACT Background In response to the substantial clinical and economic burden of diseases caused by Streptococcus pneumoniae and non-typeable Haemophilus influenzae (NTHi) in Tunisia, the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) was recently introduced into the national immunization program. However, there has yet to be a full-scale health economic analysis comparing currently available pneumococcal conjugate vaccines (PCVs) in Tunisia. Methods A Markov model that simulated the disease processes of invasive pneumococcal disease (IPD), pneumonia, and acute otitis media (AOM) over a newborn cohort lifetime was used to evaluate the cost-effectiveness/utility of PHiD-CV and the 13-valent pneumococcal conjugate vaccine (PCV13) from payer’s perspective, using 3% discounting. Vaccine effects were considered for up to 9 years of age. Results Vaccination with PHiD-CV or PCV13 was estimated to avert approximately 700 cases of IPD (200 meningitis, 500 bacteremia), and around 5,000 cases of all-cause pneumonia. However, PHiD-CV vaccination was estimated to avert around 4,000 additional AOM cases (18,000) versus PCV13 (14,000). Both PCVs were demonstrated to be cost-effective interventions, but PHiD-CV was estimated to generate additional cost savings of almost $1 million US dollars (USD) with similar levels of clinical benefits. An additional scenario which incorporated serotype-specific vaccine efficacy found no significant change in overall results. Conclusion PCVs are a cost-effective strategy to relieve the burden associated with diseases caused by S. pneumoniae and NTHi in Tunisia. PHiD-CV is more cost-effective than PCV13, generating similar health benefits, at a reduced net cost of almost $1 million USD per vaccinated cohort.