In an in-vehicle device control system, an in-vehicle device is controlled based on a checkup result of checkup operation, in which a checkup about a portable device is performed by mutual communication of transmitting a request signal from a vehicle-side unit mounted on a vehicle and transmitting in return a response signal from the portable device in response to the request signal. If the checkup is unsuccessful, the mutual communication is performed again by switching the communication frequency to perform the checkup again. When a user operates a door lock sensor, the vehicle-side unit performs an exterior checkup first. If the checkup is successful, a communication frequency, by which the checkup was performed successfully, is stored in a memory. The vehicle-side unit sets the communication frequency stored in the memory as a communication frequency, which is to be designated to the portable device, for performing an interior checkup next time.