Highways play a crucial role in Malaysia’s transportation network, connecting major urban areas and key destinations. The increases in frequency and intensity of flooding events due to climate change have caused disruptions to the highway infrastructure. Existing flood vulnerability studies typically focus on general infrastructure, such as road networks, but study specifically on highways remains limited. Unlike local roads, highways are critical for freight transport, and economic connectivity, making them highly vulnerable to flooding, which can disrupt supply chains and emergency responses. Therefore, this study aims to investigate the key variables or indicators that significantly contribute to highway flood vulnerability and the corresponding impacts and mitigation strategies for enhancement. This study employs a qualitative approach using semi-structured interviews with 15 purposively selected respondents, comprising key stakeholders in the highway industry, including representatives from highway authorities, local governments, concessionaires, and consultants, who possess specialized knowledge and experience that can contribute meaningful insights into the motivation behind the study. The interview data is then analyzed using thematic analysis. This study highlights factors contributing to highway flood vulnerability, including environmental, infrastructural, socio-economic, human activities, hydrology, climate change, education and governance. Highway flooding impacts transportation, the economy, national security, social well-being, and the environment. To implement mitigation strategies effectively, thorough planning and assessment, infrastructure improvements, management efficiency, and governance policy are essential. This study offers valuable insights for highway planners and policymakers to improve decision-making and strengthen preparedness for the increasing risks posed by climate change.