This study was planned to offer the roadmap for lifecycle clean shipping by addressing the fundamental question of ‘what are the promising energy solutions for the shipping sector?’. This goal was attempted to be achieved by a lifecycle comparative analysis of the viability of three zero-carbon fuels, ammonia, hydrogen, and inland electricity, based on the operational practicality as well as Well-to-Wake environmental impacts. Credible business scenarios were designed with a high-level screening of 27 short-route ferries currently engaged in 26 West-Scotland coastal routes. Then a series of comparative analyses between the diesel and the proposed alternative fuel sources was conducted. While carbon-free fuels are in the early stages of development in the UK, there are various views on how these fuels can be produced, distributed, and used onboard for the clean shipping economy. To determine the optimal energy solutions, all credible scenarios for the upstream pathways for these fuels were developed, based on the current and future prospected UK energy infrastructure and grids. Those scenarios were examined for West-Scotland shipping and extended to the UK targets. Their technical aspects for maritime application were also investigated in consideration of safety, regulation, infrastructural availability, supply chain constraints, barriers, and the downstream emission pathways to their uptake onboard. Ship conceptual designs were briefly conducted to evaluate the systems, technologies, and equipment required for onboard installation to utilise zero-carbon fuels. As a result of the study, when hydrogen was used as a fuel in fuel cells and electricity was supplied as a backup from batteries that store inland power and the solar PV system, GHG emissions were 25.7% of the conventional fossil fuel-using scenario. In addition, it was confirmed that GWP was 22.2% compared to MGO when ammonia was used as fuel without reforming into hydrogen and backup power was supplied from batteries and the solar PV system. It is believed that the analysis results can distinctively demonstrate the adequacy or the inadequacy of current maritime policies for decarbonising shipping. This research finally provides potential solutions for future UK maritime environmental protection and for enhancing the competitiveness of ship owners. In addition, this research concept can serve as a sample that suggests the direction of ideal research for future energy solutions in the marine sector.