In the present work, an impressed current cathodic protection (ICCP) system for the protection against corrosion of a 399-m-length container ship throughout its service life is designed. The study is carried out with the aid of a boundary element method code, accelerated by an adaptive cross approximation scheme, utilizing a detailed large-scale model. The exact geometry of the ship, the progressive damage of the coating system, and the dynamic state during the cruise of the ship are the main parameters taken into consideration in modelling. The main objective of the design process is to minimize the electric power, delivered by the ICCP system, determining the optimal number and location of the installed inert anodes to accomplish the absolute minimum protection potential on the immersed steel surfaces of the ship and, simultaneously, avoid overprotection. Performing an extensive parametric study, a six-zone ICCP system is proposed, consisting of 10 anodes at the hull and four identical anodes at each of four thrusters.