Through a systematic, holistic and transdisciplinary approach and by proposing five phases of “goal information”, “system analyzing”, “scenario construction”, “multi-criteria assessment” and “strategy building”, the study offers a process for recognizing and prioritizing energy-efficient barriers in the ship’s operational cycle according to decision-makers’ concerns. The study utilized the proposed conceptual transdisciplinary framework for overcoming energy efficiency barriers in ship operating cycles. The framework categorizes the barriers in the operational cycle into five disciplines, i.e., operations, policy and regulations, technology and innovation, human element and economics, and applies the framework to an Iranian shipping company. The results show that the economic discipline has the highest priority, and the human discipline has the least importance for the company’s decision makers. In addition, “Adverse selection” (operational discipline), “policy implementation” (policy and regulatory discipline), “split incentives” (economic discipline), “limited access to capital” (economic discipline) and “imperfect budgeting” were the main barriers to energy efficiency in the company.