A vehicle battery exchange system includes: a battery charger configured to store multiple batteries therein, and including a first battery locking device that is configured to be unlocked when each of the batteries is withdrawn from the battery charger and is configured to be locked when the batteries are stored in the battery charger, the battery charger charging a battery among the stored batteries when a state-of-charge of the corresponding battery is insufficient; and a server configured to: communicate with the battery charger and a vehicle and guiding the vehicle to a position of the battery charger when a charge request is received from the vehicle, control the first battery locking device to be unlocked when the vehicle is authenticated, and control the first battery locking device to be locked when exchange of batteries between the authenticated vehicle and the battery charger is completed.