A system for cleaning a fuel cap valve of a vehicle, may include a fuel cap having an air breather passage and a negative-pressure valve body configured for opening or closing the air breather passage; a canister for collecting evaporated gas inside a fuel tank to supply the evaporated gas into an engine intake system; and a negative-pressure control mechanism for controlling an engine negative pressure, which is applied from the engine intake system to the negative-pressure valve body of the fuel cap through the canister and the fuel tank, to reach a predetermined level or more, or for controlling the engine negative pressure at a repetition interval, in a fuel cap cleaning mode for cleaning the negative-pressure valve body of the fuel cap.