A vehicle control system includes a vehicle control apparatus mounted on a vehicle, a first portable device (electronic key) performing communication with the vehicle control apparatus, and a second portable device (smartphone) performing communication with the first portable device. The second portable device transmits, based on a predetermined operation by a user, a notification signal notifying about the operation to the first portable device. When the first portable device receives the notification signal from the second portable device, the first portable device transmits the notification signal with an identification code of the first portable device to the vehicle control apparatus. When the vehicle control apparatus detects a gesture of the user after receiving the notification signal and the identification code from the first portable device, the vehicle control apparatus extracts a feature of the gesture from a detection signal, and stores the feature to be associated with the identification code.