This study aimed to evaluate manufacturers’ perceptions of the decision-making process for new drug reimbursement and to formulate implications in operating a health technology assessment system. In 2019, we conducted a questionnaire survey and a semistructured group interview for domestic (n = 6) and foreign manufacturers (n = 9) who had vast experience in introducing new medicines into the market through a health technology assessment. Representatives of manufacturers indicated that disease severity, budget impact, existence of alternative treatment, and health-related quality of life were relevant criteria when assessing reimbursement decisions. Compared with domestic manufacturers, foreign manufacturers were risk takers when making reimbursement decisions in terms of adopting a new drug and managing pharmaceutical expenditure. However, foreign manufacturers were risk-averse when evaluating new drugs with uncertainties based on real-world data such as clinical effectiveness. Based on manufacturers’ perceptions of the decision-making process for new drug reimbursement, there is room for improvement in health technology assessment systems. Explaining the underlying reasons behind their decisions, unbiased participation by various stakeholders and their embedded roles in the decision-making process need to be emphasized. However, the measures suggested in this study should be introduced with cautions. The process of health technology assessment might be a target for those who undermine the system in pursuit of their private interests.