Fossil fuel combustion is a major source of Greenhouse Gases (GHGs), which cause global warming. To prevent further increases in anthropogenic GHGs, the global community needs to take action in each segment of the economy, including the shipping sector. Among different measures for reducing shipping emissions, the most promising one is the replacement of conventional marine fuels with alternatives. According to the International Maritime Organisation’s regulations, ships engaged in international shipping need to reduce their annual emissions by at least 50% by 2050. However, this does not apply to fishing vessels, which are highly dependent on fossil fuels and greatly contribute to air pollution. This paper investigates the environmental footprint of a fishing vessel (purse seiner) through the implementation of various alternative fuels. Within the research, Life-Cycle Assessments (LCAs) and Life-Cycle Cost Assessments (LCCAs) are performed, resulting in life-cycle emissions and lifetime costs for each alternative, which are then compared to a diesel-powered ship (baseline scenario). The comparison, based on environmental and economic criteria, highlighted methanol as the most suitable alternative for the purse seiner, as its use onboard resulted in 22.4% lower GHGs and 23.3% lower costs in comparison to a diesel-powered ship.