OBJECTIVES: Several decision support tools have been developed to aid policy decision making regarding the adoption of pneumococcal conjugate vaccine (PCV) into national immunization programs. Lacking critical evaluation of the tools causes decision makers difficulties in understanding and feeling ownership of information resulting from the tools, particularly in resource poor countries where technical capacity is lacking. This study aims to critically compare decision making tools and their cost-effectiveness (CE) findings, and to identify influential parameters in the models. The overall objective is to provide decision makers with a menu of CE tools and their characteristics for their optimal use rather than to recommend a single model.   METHODS: The WHO requested access to publicly available CE tools for PCV from both public and private provenance. All tools were assessed according to WHO’s economic evaluation guideline. All key attributes and characteristics were compared. A series of sensitivity analyses were performed to determine the major drivers of the models. The results were compared using a standardized set of input parameters. RESULTS: Three CE tools, including PAHO ProVac’s TriVac, PneumoADIP and GSK’s SUPREMES tools, were provided. They all compared the adoption of PCV into national immunization program with no immunization. The models differed in terms of attributes, structure, and data requirement, but captured similar range of diseases. Herd effect was estimated using different approaches. The main driving parameters were vaccine efficacy against pneumococcal pneumonia, vaccine price and coverage, serotype coverage and disease burden. With a standardized set of input parameters, TriVac and PneumoADIP provided similar findings including incremental costs, outcome and incremental cost-effectiveness ratio. CONCLUSIONS: Models differed in terms of model structure and key assumptions. Vaccine price and efficacy were the most influential parameters. Understanding differences and similarities of CE tools could provide policy makers more efficient use for aiding their decision making process.