A system of charging a battery of a vehicle is provided. The system includes a charger having a direct current (DC) capacitor to which a DC voltage converted from an AC charge voltage is applied and a first DC converter that converts a magnitude of a voltage of the DC capacitor. A first battery is connected to the first DC converter and is charged with a DC voltage converted by the first DC converter. A second DC converter is connected to the battery and converts a magnitude of a voltage of the battery. A second battery receives a DC voltage converted by the second DC converter. A controller charges the DC capacitor up to a predetermined initial charge voltage using power stored in the second battery by operating the second DC converter and the first DC converter in a backward direction before the AC charge voltage is provided to the charger.