With the strengthening of international environmental regulations, many studies on the integrated electric propulsion systems applicable to eco-friendly ship are being conducted. However, few studies have been performed to establish a guide line for the overall pure electric propulsion ship design. Therefore, this paper introduces the comprehensive design of DC shipboard power system for pure electric propulsion ship based on battery energy storage system (BESS). To design and configure the pure electric propulsion ship, 2 MW propulsion car ferry was assumed and adopted to be the target vessel in this paper. In order to design the overall system, a series of design processes, such as the decision of the ship operation profile, BESS capacity selection, configuration of the power conversion systems for propulsion, battery charging/discharging procedures, classification of system operation modes, and analysis of the efficiency, were considered. The proposed efficient design and analysis of the pure electric propulsion ship was qualitatively and quantitatively validated by MATLAB Simulink tool. The methodology presented in this paper can help design real ships before the system commissioning.