Ships can be operated more efficiently by utilizing intelligent decision support integrated with onboard data collection systems. In this study, a Bayesian optimization-based decision support system, which utilizes ship performance models built by machine learning methods, is proposed to help determine the operational set-points of two engines for double-ended ferries. By optimizing the ferries’ power allocation between the stern and bow engines, the Decision Support System (DSS) will simultaneously attempt to keep the ETA of the ferry fixed under a set of operational constraints using the Bayesian optimization. Its objective is to minimize fuel consumption along individual trips. Based on simulation environment, the DSS can reduce at maximum 40 % fuel consumption with no significant change of the ETA. Final full-scale experiments of a double-ended ferry demonstrated an average of 15 %, where at least half of this saving was achieved by the optimized power allocation between bow and stern engines.