This paper presents an adaptive protection scheme that adapts overcurrent-relaying functions to changes in shipboard power system topologies initiated by reconfiguration functions. Reconfiguration is an energy management function used by shipboard power systems to alter system topology to meet operational requirements. The adaptive protection scheme uses the data of the system to determine whether any changes have occurred in the system topology and/or load and generator capacities. If there is a change, power-flow and fault-analysis are performed on the system. The results are used to update the system overcurrent relays. The scheme was tested on a two-bus power system and the results were validated in CAPE software.