The fishing sector is faced with emission problems arising from the extensive use of diesel engines as prime movers. Energy efficiency, environmental performance, and minimization of operative costs through the reduction of fuel consumption are key research topics across the whole maritime sector. Ship emissions can be determined at different levels of complexity and accuracy, i.e., by analyzing ship technical data and assuming its operative profile, or by direct measurements of key parameters. This paper deals with the analysis of the environmental footprint of a fishing trawler operating in the Adriatic Sea, including three phases of the Life-Cycle Assessment (manufacturing, Well-to-Pump (WTP), and Pump-to-Wake (PTW)). Based on the data on fuel consumption, the viability of replacing the conventional diesel-powered system with alternative options is analyzed. The results showed that fuels such as LNG and B20 represent the easiest solution that would result in a reduction of harmful gases and have a positive impact on overall costs. Although electrification and hydrogen represent one of the cleanest forms of energy, due to their high price and complex application in an obsolete fleet, they do not present an optimal solution for the time being. The paper showed that the use of alternative fuels would have a positive effect on the reduction of harmful emissions, but further work is needed to find an environmentally acceptable and economically profitable pathway for redesigning the ship power system of fishing trawlers.