This paper investigated the opportunities and challenges of integrating ports into hydrogen (H2) supply chains in the context of Australia and Japan because they are leading countries in the field and are potential leaders in the upcoming large-scale H2 trade. Qualitative interviews were conducted in the two countries to identify opportunities for H2 ports, necessary infrastructure and facilities, key factors for operations, and challenges associated with the ports’ development, followed by an online survey investigating the readiness levels of H2 export and import ports. The findings reveal that there are significant opportunities for both countries’ H2 ports and their respective regions, which encompass business transition processes and decarbonisation. However, the ports face challenges in areas including infrastructure, training, standards, and social licence, and the sufficiency and readiness levels of port infrastructure and other critical factors are low. Recommendations were proposed to address the challenges and barriers encountered by H2 ports. To optimise logistics operations within H2 ports and facilitate effective integration of H2 applications, this paper developed a user-oriented working process framework to provide guidance to ports seeking to engage in the H2 economy. Its findings and recommendations contribute to filling the existing knowledge gap pertaining to H2 ports.