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The backup power system (BPS) is essential to data centers (DCs) in case of grid outage. Currently, the diesel generator (DG) is the most commonly used solution. However, due to the need of decarbonization, fuel cells (FCs) are emerging as a promising alternative. This paper conducts a holistic economic analysis to investigate the benefit from using FCs to replace DGs, which takes into account more key impact factors. Different requirements by different Tiers of DCs, such as on the BPS runtime and the BPS test time, are considered. Under the benchmark condition, i.e. 800 USD/kW for the FC capital cost, 4.8 USD/kg, 1.25 USD/L and 90 USD/ton for hydrogen, diesel, and CO2 prices, the payback period is 13.4 years and 13.1 years when using FCs to replace DGs for Tier 1–2 DCs and Tier 3 DCs. Since Tier 4 DCs require more units, FCs can be economically feasible if the FC capital cost reduces by 20.3 %, the diesel price increases by 19.7 %, or the green hydrogen price decreases by 35.5 %, compared to the benchmark conditions. Among the factors, the FC capital cost, the diesel price, and the hydrogen price are found to affect the payback period mostly.