A system and method for configuring an intelligent electronic device (IED) from a plurality of IEDs connected in a communication network of a substation with a computing system includes a computing system communicatively connected in the communication network of the substation for transmitting a configuration of at least one application function to the IED for operating an electrical equipment in the substation. The method for configuring the IED comprises using a virtual model of the IED to generate the IED configurations through a simulation that involves a sequence prediction technique. The sequence prediction technique facilitates generating a sequence of functions arranged in an order and sequentially determining connections between at least one input and at least one output of the one or more functions that comprises the application function. The generated sequence of functions and sequence of connections constitute the IED configuration corresponding to a given application function.