A wireless charger output protection system and method is provided for protecting a battery in an electric vehicle during wireless charging from both a desired power source and a stray power source. A wireless power transfer system includes a wireless charger on the electric vehicle side that receives power wirelessly from a charging base. The wireless charger output protection system and method shuts down the wireless charger output and dumps energy in a receive antenna (e.g., a vehicle pad) when a low-voltage battery connected to the wireless charger is lost. The wireless charger output protection system and method also shuts down the wireless charger output and dumps unwanted energy in the receive antenna (e.g., a vehicle pad) when power is transferred from a stray power source coupled to the receive antenna.