A power source system may include a main power source, a power converter including a capacitor, a relay configured to switch between connection and disconnection between the power converter and the main power source, an auxiliary power source, a boost converter having a low voltage terminal thereof connected to the auxiliary power source, and having a high voltage terminal thereof connected to the power converter without interposing the relay, and a controller configured to pre-charge the capacitor prior to placing the relay in a connected state when a main switch of a vehicle is turned on. The controller may be configured to store a peak value of a current of the auxiliary power source in a memory of the controller, and start to pre-charge the capacitor when a current of the auxiliary power source falls from the peak value by more than a predetermined current difference.