Fuel cells aboard hybrid electric vehicles (HEVs) are often hybridized with an energy storage system (ESS). Batteries and ultracapacitors are the most common technologies used in ESSs aboard HEVs. High-speed flywheels are an emerging technology with traits that have the potential to make them competitive with more established battery and ultracapacitor technologies in certain vehicular applications. This study compares high-speed flywheels, ultracapacitors, and batteries functioning as the ESS in a fuel cell based HEV on the bases of cost and fuel economy. In this study, computer models were built to simulate the powertrain of a fuel cell based HEV where high-speed flywheels, batteries, and ultracapacitors of a range of sizes were used as the ESS. A simulated vehicle with a powertrain using each of these technologies was run over two different drive cycles in order to see how the different ESSs performed under different driving patterns. The results showed that when cost and fuel economy were both considered, high-speed flywheels were competitive with batteries and ultracapacitors.