The commercialisation of research and development (R&D) outputs and intellectual property (IP) has become a strategic priority in Malaysia’s higher learning institutions (HLIs) in support of innovation-led economic growth. Despite sustained public investment in research funding, patent filings, and academic output, the translation of university-generated technologies into licensing agreements, spin-offs, and market-ready solutions remains limited. This study examines the systemic barriers that constrain R&D and IP commercialisation in Malaysian HLIs by adopting a qualitative document-based systemic analysis supported by descriptive trend interpretation of commercialisation indicators. The analysis draws on policy documents, institutional reports, and established scholarly literature to identify recurring structural weaknesses across five interrelated domains: policy and governance, institutional incentive systems, technology transfer office (TTO) functions, industry engagement, and commercialisation funding mechanisms. The findings indicate that weak commercialisation performance is not caused by isolated constraints alone, but by reinforcing interactions among publication-oriented academic incentives, administratively focused TTO structures, delayed industry participation, fragmented funding pathways, and weak strategic IP portfolio management. These interconnected barriers reduce the likelihood that university-generated IP will progress into sustainable commercial outcomes. In response, the paper proposes a systemic mitigation framework centred on incentive realignment, capability upgrading of TTOs, early co-creation with industry, strategic IP governance, and stronger ecosystem coordination. The study contributes a policy-relevant and institutionally actionable perspective for strengthening university-based innovation commercialisation in Malaysia.