A method for initializing expended modules in PLC (Programmable Logic Controller) system is provided in which an initialization request signal is generated and transmitted to a plurality of expended modules, when one basic unit initializes a plurality of expended modules, and an initialization completion signal is sequentially transmitted by the plurality of expended modules, when the initialization is completed, whereby the initialization time can be optimized, the method including performing an initialization operation after generating, by a basic unit, an initialization request signal and transmitting the initialization request signal to a plurality of expended modules, and determining that the initialization operation is completed, when an initialization completion signal is received from the expended modules connected to the basic unit.