Microgrid is a group of interconnected generating units and loads at the distribution level which operates in two modes—Grid connected mode and Islanded mode. Fault clearance in a microgrid is a key challenge for protection engineers. This paper aims to identify the best fit relay suitable for a microgrid using modified cuckoo search algorithm based on key parameters like current rating, Time Multiplier Setting (TMS), Plug Setting Multiplier (PSM) and time of operation (top). This algorithm aids in providing suitable relay coordination in microgrid and clears the faulty portion of network effectively from the healthy portion of network. © Springer Nature Singapore Pte Ltd. 2017.