To provide a system and a method for cleaning a filter medium which can surely and uniformly clean the filter medium by removing stains stuck to the filter medium according to the quality of the filter medium and the qualities of the stains.

The system for cleaning the filter medium is constituted in such a way that a main pressurized water supply line for supplying high-pressure cleaning water to a jet pump for sucking the filter medium from a pressure pump is branched, a branched assistant pressurized water supply line is connected to an auxiliary jet pump, a discharge port of the auxiliary jet pump is communicated with a sorting portion while interposing a supply line which is used for connecting a discharge port of the jet pump for sucking the filter medium to the sorting portion, between them or communicated directly with the sorting portion, and a water flow rate control means for controlling a flow rate of the high-pressure cleaning water is arranged on each of the main pressurized water supply line and the assistant pressurized water supply line.