ABSTRACT Background: Decision-making processes regarding new vaccine prioritizations are complex. The objective of this study was to prioritize the introduction of new vaccines in Indonesia. Methods: A multi-criteria decision analysis (MCDA) was applied in this study. A preliminary data collection form was developed to collect country-specific data in relation to 30 pre-defined attributes. In particular, an open-ended questionnaire was conducted among targeted respondents from global level, national level and vaccine manufacturers, which were involved in the financial flows of new vaccine procurement in Indonesia. For setting new vaccines priorities, targeted respondents were asked to assign weight on 10 selected criteria. Results: Top 3 attributes with the highest weight from respondents were premature deaths averted per year, incident cases prevented per year, and cost-effectiveness. Applying criteria scores and weight assessment, the result showed that PCV, rotavirus, HPV, and JE would be on the 1st, 2nd, 3rd, and 4th rank for setting new vaccine priority in Indonesia. There was a significant difference score (p value <0.05) between all these vaccines. Conclusions: PCV, rotavirus and HPV vaccines should be more prioritized than JE vaccine. This ranking is in line with the WHO’s priority list, which potentially illustrates the validity and usefulness of our MCDA-approach.