This study investigated the economic feasibility of introducing a new energy system, the greenhouse–fuel cell convergence system (GFCS), to a greenhouse that consumes a lot of energy. The GFCS is a concept that uses the heat generated during the power generation process to cool and heat the greenhouse, uses the emitted CO2 as fertilizer inside the greenhouse, and sells the generated electricity. For economic evaluation, the annual energy consumption of the greenhouse was first calculated through simulation, and then the appropriate fuel cell capacity was determined. Next, a farmer-led business model and a utility-led business model were presented, and the economic feasibility of these models was evaluated for tomatoes and mangoes. The economic evaluation of the GFCS confirmed the economic feasibility by comparing it with a greenhouse equipped with a geothermal heat pump. The results of the economic evaluation revealed that the farmer-led model had a benefit–cost ratio (B/C) ranging from 0.62 to 0.65 even with government support for heat utilization facilities, which was lower than that of a typical greenhouse (1.03 to 1.06). On the other hand, the utility-led model showed high B/C ranging from 1.19 to 1.86. If the initial investment cost of the fuel cells is reduced and a government policy is appropriately supported, the GFCS can be economically applied to greenhouses.