The optimization of the hull–propeller system of a ship has always been one of the most important aspects of design in order to reduce the costs, mechanical losses and increase the life of system components. The proposed design methodology represents a comprehensive approach to optimize the hull–propeller system simultaneously. In this study, two objective functions are considered, i.e. lifetime fuel consumption (LFC) and lifetime cost function (Cost). The mission profile of the vessel is adopted to minimize the LFC and Cost over their operational life. The well-known evolutionary algorithm based on NSGA-II is employed to handle the multi-objective problems, where the main propeller and hull coefficients are the unknown and are considered as design variables. The results are presented for a commercial container ship driven by B-series propeller. Three different engines with the same mission profile were taken and the results revealed that the proposed method is an appropriate and effective approach for finding Pareto optimal solutions distributed uniformly and is able to improve both of the objective functions significantly and other performances of the system.