This study proposes an operation planning method for polymer electrolyte fuel cell cogeneration systems (PEFC-CGSs). PEFC-CGSs provide hot water by utilizing waste heat produced in the electricity generation process. An appropriate operation plan according to household demand will lead to further energy saving. The authors have discussed a framework for estimating expected operation costs of individual operation plans to select an appropriate candidate that minimizes the cost. In this scheme, the expected cost under each corresponding operation was independently estimated. This approach can be expected to provide accurate prediction of costs under individual operations. However, one open issue remains; it may not work well in estimating relative goodness compared to other operations. In this study, the authors propose a new cost estimation approach, focusing on relative appropriateness in candidate plans based on a multiple output prediction. The usefulness of the proposed approach is proved via a numerical simulation.