A vehicle control system includes a tracking unit and a function unit cooperating therewith. The tracking unit may include a vehicle position determining device, a wireless communications device, and a tracking controller cooperating with the vehicle position determining device and the wireless communications device to send vehicle position information to a user. Further, the function unit may include at least one uniquely coded transmitter to be carried by a user, a receiver at the vehicle for receiving signals from the at least one uniquely coded transmitter, and a function controller at the vehicle and connected to the receiver for learning the at least one uniquely coded transmitter to permit control of a vehicle function by the user. The function controller may advantageously cooperate with the wireless communications device of the tracking unit for sending an alert indication of whether at least one new uniquely coded transmitter has been learned.