Carbon emissions generated by the transportation sector represent a large part of total greenhouse gas emissions and are thus subject to various policies and initiatives for emission reduction and the development of sustainable transportation networks. Furthermore, passenger transportation generates a significant amount of emissions within this sector, especially in those countries with large and developed tourist sectors. Examples of such countries are Italy and Croatia, located in the Adriatic region, with a large portion of passengers between them being transported utilizing mainly maritime and/or road transportation modes. A proper analysis of the impact of these transportation mode choices on carbon emissions is essential to enable the selection of the optimal transportation mode for the particular transportation route with respect to the generated emissions. Therefore, this study determines the carbon emissions of the maritime and/or road transportation modes on the existing cross-border passenger transportation routes between Italy and Croatia. For the analysis, the Adriatic region was divided into three sections—the Northern, Middle, and Southern regions—each characterized by specific transportation routes defined by geographical features and distances. The results obtained from this research are presented as total carbon emissions for each transportation mode separately, based on each of three chosen routes in different regions. In addition, a carbon emission comparison between each transportation mode in regard to occupancy rate is performed and presented separately for each chosen route based on its specific distances, transportation means, and features. Finally, by providing an analysis of the existing state, this study can serve as a basis for Italy–Croatia cross-border passenger mobility network modernization and the introduction of new, sustainable, and multimodal transportation routes.