The first part of the current study highlights the importance of developing a clean hydrogen supply chain (CHSC) in Iran to enhance energy security and contribute to global efforts towards sustainable energy transition. Depending on whether the focus is on domestic consumption or export of hydrogen, the study provides valuable insights into the prioritization of CHSC development pathways via multi-criteria decision-making tools (AHP, AHOP-TOPSIS, and AHP-VIKOR). The results show that for domestic hydrogen consumption (internal scenario), the best path of the supply chain includes blue hydrogen from steam methane reforming coupled with carbon capture and storage, H2-carriers (ammonia and methanol), natural gas grid for transportation and distribution, and industry sector as the end user. In the external scenario, however, the best path of the CHSC consists of green hydrogen production based on solar energy, and the other parts of the path include liquid hydrogen as the storage method, ship as the distribution and transportation, and industrial sector as the end user. By identifying the most suitable methods and technologies for each stage of the supply chain, this paper offers a comprehensive analysis that can guide decision-making in CHSC development.