The fail safe apparatus for an eco-friendly vehicle includes: a main battery to supply driving power of a vehicle; a battery controller to manage a state of charge of the main battery; a power converter to convert power supplied from the main battery into power for charging an auxiliary battery; a motor controller to drive a motor with the power supplied from the main battery; a hybrid starter generator to start an engine and charge the main battery; and a vehicle controller to monitor a capacity voltage of any one of the power converter and the motor controller when there is an error in data communication of the battery controller and control charging and discharging of the main battery based on the monitored results.