Owing to the stringent regulations on pollutant emissions that are imposed by the International Maritime Organization and increasing fuel prices, there has been significant research on developing cleaner fuels and novel propulsion systems. This study presents a techno-economical and risk assessment method for evaluating alternative propulsion technologies and cleaner fuels as substitutes for heavy fuel oil and two-stroke diesel engines in marine transportation. This analysis was carried out for two different journeys. Accordingly, we evaluated the economic benefits of using an enhanced intercooler/reheat combined gas and steam cycle or simple and intercooler/reheat combined gas and steam cycles that were fueled by marine diesel oil or liquified natural gas instead of a two-stroke diesel engine that was fueled by MDO as the propulsion system in a large container ship, considering different shipping routes. The results highlighted the advantages of implementing the simple, intercooler/reheat, and enhanced combined gas and steam cycles as propulsion systems. A sensitivity analysis was performed to investigate the effects of the fuel cost, capital cost, and hull fouling resistance on the economic analysis. For the routes that were considered herein, compared to a two-stroke diesel engine that was fueled by MDO, the simple, intercooler/reheat, and enhanced gas and steam combined cycles that were fueled by LNG increased the net present value by 78.3%, 78.5%, and 76.4%, respectively, and reduced the payback period by 38.8%, 38.9%, and 35%, respectively. Furthermore, the fuel and capital costs had a significant influence on the overall economic profit.