Decarbonization is the most urgent task for the shipping industry. The International Maritime Organization, which makes the rules for shipping companies, has strengthened their carbon emissions regulation in order to reduce emissions to 70% of 2008’s carbon emissions by 2050. However, 75% of the existing fleet cannot satisfy this carbon emission regulation. The building of new vessels makes it possible to reduce carbon emissions and satisfy this regulation through adopting eco-friendly propulsion methods, such as LNG, ammonia, and methanol propulsion. However, the existing vessels on the sea find it difficult to dock and change their propulsion equipment. This research aims to propose a novel voyage operation method—a just-in-time arrival policy—that converts vessels’ waiting time into voyage time. The proposed method can reduce carbon emissions without propulsion system alteration and expand a vessel’s lifespan, thus satisfying carbon regulations. The carbon intensity indicator, invented by the IMO to regulate vessel carbonization, assesses the quantity of reduced carbon emissions. This research investigated the variation in the carbon intensity indicators of vessels when the just-in-time arrival policy was applied through studying an actual vessel’s arrival and departure dates at the Pusan International container terminal. According to the results of our analysis, ship carbon emissions decreased by an average of 45.8%, and by a maximum of 91%, compared to the levels before applying the proposed method. In addition, 87.0% of vessels obtained a carbon intensity indicator rank improvement and expanded the period that can satisfy the carbon intensity regulation by an average of eleven years and a maximum of twenty-seven years through applying the proposed just-in-time arrival policy. Additionally, the improvement effect of the carbon intensity rank positively correlates with ship size and waiting time at the port.