A system of controlling an output of a high voltage battery for an eco-friendly vehicle includes: the high voltage battery mounted in the eco-friendly vehicle; a storage configured to store information on maximum available charge and discharge power according to a temperature and a state of charge (SOC) of the high voltage battery; and a controller configured to control available charge power and available discharge power of the high voltage battery based on at least one of information on a charge duration and a discharge duration of the high voltage battery, information on an accumulated charge amount and an accumulated discharge amount of the high voltage battery, and information on a requested output amount of the vehicle.