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In the maritime domain, hydrogen fuel cell propulsion and autonomous vessels are two important issues that are yet to be implemented together because of a few challenges. It is obvious that there are several individual safety studies on Maritime Autonomous Surface Ships and hydrogen storage as well as fuel cells based on various risk assessment tools but the combined safety studies that include hydrogen fuel cells on autonomous vessels with recent risk analysis methods are extremely limited. This research chooses the "System-Theoretic Process Analysis" (STPA) method which is a recent method for potential risk identification and mitigation. Both hydrogen and autonomous vessels are analyzed and assessed together with the STPA method. Results are not speculative but rather flexible compared to conventional systems. The study finds a total of 44 unsafe control actions (UCAs) evolved from human and central control unit controllers through STPA. Further, the loss scenarios (LS) are identified that lead to those UCAs so that loss scenarios can be assessed and UCAs can be mitigated for safe operation. The objective of this study is to ensure adequate safety for hydrogen fuel cell propulsion on autonomous vessels. [ABSTRACT FROM AUTHOR]