In an in-vehicle device control system, a vehicle-side unit mounted in a vehicle controls an in-vehicle device in accordance with a result of checkup about a portable device performed by mutual communications, in which the portable device returns a response signal in response to a request signal transmitted from the vehicle-side unit. An ECU of the vehicle-side unit checks whether it is a regular checkup timing, and performs an exterior checkup if it is determined to be the regular checkup timing. The ECU sets in this case a communication frequency, which is higher in priority order, as a communication frequency to be designated to the portable device.