BACKGROUND: The Moldovan health authorities introduced the 13 valent pneumococcal conjugate vaccine into the national immunization schedule for children in 2013. This study aimed to evaluate the cost-effectiveness of the pneumococcal conjugate vaccine compared to a no-vaccination strategy in children under 5 Years of age in the Republic of Moldova. METHODS: We used UNIVAC (version 1.7), a static decision model, to evaluate the health and economic outcomes of vaccination in a single-cohort of children under five years. We modeled vaccine introduction over 10 birth cohorts starting in 2013. We assumed a 2+1 (two doses + booster) schedule and a vaccination price of US16.34 per dose. We used locally-specific data for pneumonia incidence, mortality, treatment, and costs. Model outcomes included pneumonia cases, hospitalizations, deaths, disability-adjusted life years, and costs presented in USD. Cost-effectiveness was reported as Incremental Cost Effectiveness Ratio. The Incremental Cost Effectiveness Ratio was calculated to estimate the additional cost to save an additional life year. RESULTS: From the governmental health sector the Incremental Cost Effectiveness Ratio was 939 and from society perspective, 272, respectively. Withal cost per disability-adjusted life years (DALY) averted was US6311. PCV-13 was projected to prevent 2310 hospitalizations due to pneumococcal disease, including 118 deaths. Vaccination could potentially reduce the highest treatment cost from the payer perspective at 4 081 412 for the 13 valent pneumococcal conjugate vaccine. CONCLUSION: This study evidenced that cost per DALY averted is US6311, which is between one and three times Gross Domestic Product (GDP) per capita, these findings extrapolate PCV-13 as a cost-effective intervention. Considering the scenario of Republic of Moldova the PCV program is a cost effective intervention and justifies the introduction of PCV into routine immunization schedule throughout the country in order to reduce morbidity and mortality among the under-five-year-old children.