This study involves investigation of fuel cell hybrid vehicles. The main power source in the dynamic configuration is a proton exchange membrane fuel cell. An energy performance comparison is conducted between the use of a lithium-ion battery (Automotive Energy Supply Corporation, Japan) and the UltraBattery (Furukawa Battery Company, Japan) as auxiliary power sources. The MATLAB/Simulink for simulation is used to observe dynamic behavior and overall performance. This study describes the simulation frameworks of the proton exchange membrane fuel cell, ultracapacitor, lead-acid battery, and UltraBattery. Then, the Economic Commission for Europe 40 driving cycle is used to test and investigate the performance of the fuel cell hybrid vehicle. Four energy output models are adopted to simulate the energy demand and the energy motor output of the dual power source, namely the high-load demand, general demand, low-load demand, and charge models. The simulation results indicate that the lithium battery recycles 0.1% more work compared with the UltraBattery. Regarding fuel economy, the UltraBattery is only 0.1% inferior to the lithium battery. The expected cost of an UltraBattery with the same specifications is 35% less than that of a lithium battery. Considering fuel economy and cost simultaneously, the UltraBattery can compete with the lithium battery. Copyright (C) 2015 John Wiley & Sons, Ltd.