A system and method for charging a plug-in hybrid vehicle can improve the on-board charging efficiency of the plug-in hybrid vehicle by adjusting a frequency of operation of a cooler when cooling an on-board charger (OBC) by circulating coolant when the temperature of the OBC rises while a high-voltage battery is being charged. The operations of a water pump and a radiator fan are controlled by determining whether the voltage of the high-voltage battery is within or out of a reference voltage range in which the on-board charging of the high-voltage battery is performed. This consequently prevents power from being unnecessarily consumed by operation of the cooler, such that the efficiency of charging is improved and the OBC is properly cooled.