Traditionally, the environmental performance of marine systems in terms of exhaust emissions has never been among the primary concerns of the maritime industry. However, this situation is going to quickly change, as in the shipping sector Energy Efficiency Design and Operation IMO Indexes testify. In such a context it is worth mentioning that the greening of shipping operations can be effectively achieved by a suitable system design and energy management. Ship Energy Efficiency Management Plan (SEEMP) should be a tool to monitor and to optimize ship and fleet efficiency performance; as a consequence it will have a deep impact on the reduction not only of the exhaust gas emissions but also of the operational costs. To reach this goal energy modelling represents the keyword. In particular, the estimate by simulation, of onboard power generation, consumption and losses plays a fundamental role for driving, for instance, a decision support tool toward the optimal choices as far as energy management is concerned. To this purpose, in the paper the authors present the outcomes of the activities carried out to develop a simulation tool able to represent an overall ship system from the energetic point of view. Modelling approach and the results of numerical simulations performed by the authors to estimate vessel fuel consumption in a real case study are shown and discussed.