Fuel cells are electrochemical devices that are conventionally used to convert the chemical energy of fuels into electricity while producing heat as a byproduct. High temperature fuel cells such as molten carbonate fuel cells and solid oxide fuel cells produce significant amounts of heat that can be used for internal reforming of fuels such as natural gas to produce gas mixtures which are rich in hydrogen, while also producing electricity. This opens up the possibility of using high temperature fuel cells in systems designed for flexible coproduction of hydrogen and power at very high system efficiency. In a previous study, the flowsheet software Cycle-Tempo has been used to determine the technical feasibility of a solid oxide fuel cell system for flexible coproduction of hydrogen and power by running the system at different fuel utilization factors (between 60 and 95%). Lower utilization factors correspond to higher hydrogen production while at a higher fuel utilization, standard fuel cell operation is achieved. This study uses the same basis to investigate how a system with molten carbonate fuel cells performs in identical conditions also using Cycle-Tempo. A comparison is made with the results from the solid oxide fuel cell study.