Microgrid caters to the growing power demand in the distribution network. Due to reconfiguration of microgrid, conventional protection schemes are not suitable for fault clearance. This paper proposes a communication assisted central protection system (CPS), which monitors the microgrid. The active nodes of the network are populated using Bellman Ford algorithm. In the event of fault, the Dijkstras algorithm is employed on the current topology of network, to identify the shortest path from the faulted point to the point of common coupling. This hybrid algorithm ensures that during fault clearance, minimum portion of network disconnection occurs. The algorithm is tested and validated on 40-bus and 54-bus microgrid network. © 2016 American Scientific Publishers. All rights reserved.