This paper presents a distributed Flywheel Energy Storage System (FESS) for mitigating the effects ofpulsed loads such as those exist in Shipboard Power Systems (SPS). A comparison betweendistributed and centralized allocation of FESS was provided with and without the utilization of ultra-capacitors on the DC side. A model for hybrid AC/DC SPS with zonal distribution architecture was built in a simulation software. In order to accurately evaluate the performance of the system, three different case studies are presented with and without the FESS. The results of each case are analyzed and discussed. It can be shown that the distributed allocation of FESS can reduce the overloading on the generators and frequency fluctuations.