One of the most important devices in an underwater vessel is a propulsion system. It should be a quiet andefficient system for stealthy operations in the large mission area. Hence lead-acid battery system has been used tosupply the energy to electric motor. Recent technological developments and improvements, such as polymerelectrolyte membrane(PEM) fuel cell and lithium polymer battery and have created the potential to improve overallpower and propulsion performance. An underwater vessel always starts their mission with a limited energy and isnot easy to refuel. Therefore design of energy elements, such as fuel cell and battery, and their load distributionare important to increase the maximum operating time of underwater vessel. In this paper, the lead-acidbattery/PEM fuel cell and lithium polymer battery/PEM fuel cell were suggested as propulsion system and theirperformances were analyzed by modeling and simulation using Matlab/Simulink. Each model concentrated onrepresenting the characteristics of energy element depending on demand current. As a result the effect of loaddistribution between battery and fuel cell was evaluated and the operation time of each propulsion system was ableto be estimated exactly.