Hydrogen is considered a key enabler for energy transition, offering a clean alternative to fossil fuel, and its applications span different sectors, including transportation, the manufacturing industry, power generation, and many others. Despite the capabilities, shifting energy to hydrogen remains complicated. The hydrogen supply chain deployment faces numerous challenges, including infrastructure limitations, cost constraints, technological hurdles, regulatory barriers, and market uncertainties. Oman's move to renewable energy and the implementation of large-scale green hydrogen generation is expected to reduce high reliance on fossil fuels and contribute to the country's socio-economic. This study conducted 21 interviews with energy and supply chain specialists in Oman to validate the literature review findings regarding hydrogen supply chain challenges. This paper uses thematic analysis to address the challenges associated with the hydrogen supply chain in Oman. The initial template is created based on the literature study and updated according to the interview results. The thematic analysis yielded three themes and sub-themes totaling eight. The upstream challenges identified are sourcing, production, regulation, and technology. The second theme addresses midstream challenges, focusing on the transportation and storage issues of the hydrogen supply chain. The final theme focuses on downstream challenges related to demand and regulations. Demand highlights the influence of social preferences and awareness, as the high cost of hydrogen can discourage consumer adoption. Additionally, the Analytical Hierarchy Process (AHP) was performed to rank the identified challenges, allowing stakeholders to focus on the most critical and solvable issues in the deployment of green hydrogen.