Purpose The government support for research and development (R&D) initiatives in the pharmaceutical sector has been declining. The purpose of this study is to analyze factors influencing the efficacy of government R&D support programs directed at pharmaceutical enterprises in South Korea, aiming to provide valuable insights for policymakers responsible for resource allocation in the pharmaceutical industry. Design/methodology/approach The study uses data from 490 R&D projects conducted by 106 pharmaceutical enterprises between 2018 and 2020, sourced from the National Technical Information Service and Drug Approval Research and Technology repositories. The data were analyzed using negative binomial regression analysis operated by the Statistical Package for the Social Sciences. Findings Applied research, cooperative research and the number of doctoral researchers positively impact both the quantitative and qualitative performance of the papers. The number of doctoral researchers, government research funds and the ratio of private investment to total R&D investment positively impacted the quantitative and qualitative performance of patents. However, enterprise age negatively affected patent performance. Notably, sales were significantly associated with patent qualitative performance but not with patent quantitative performance. Originality/value While previous studies have primarily focused on specific types of government R&D support or individual sectors, this study provides a broader perspective by incorporating a variety of variables, to examine the overall performance of government R&D programs in the pharmaceutical sector. This paper addresses the growing concern over declining government support and offers insights that were not fully explored in prior studies. By doing so, this research highlights the importance of understanding how diverse factors collectively influence the effectiveness of government R&D support, providing new directions for innovation and excellence in the pharmaceutical industry.