Shipping is a major contributor to total global CO2 emissions. In recent years, various operational and technical measures have been proposed to decarbonize the shipping sector. The cost-effectiveness of these mitigation measures is usually evaluated on an individual basis. However, the cost-effectiveness of individual measures could be influenced by the presence of other measures (when selected simultaneously) used to meet the decarbonization targets. As such, it is important to take into consideration such interdependencies when ranking and selecting the mitigation measures. In response to this problem, we propose a method to systematically rank and select the mitigation measures whose cost and carbon abatement potentials depend on the presence of one another. The proposed method is also capable of accounting for uncertain input factors, such as implementation costs and fuel costs. Through a case study considering a set of 14 measures, findings from our study demonstrate the importance of considering the interdependencies of these mitigation measures. We further conduct a sensitivity analysis, in order to ascertain the influence of the relevant input parameters.