Disclosed are a portable refrigerator with a fuel cell system and an operating method thereof. The portable refrigerator with a fuel cell system comprises a case having a storage space, a fuel cell stack disposed in the case, a gas tank configured to store gas necessary to operate the fuel cell stack, a fan configured to cool the fuel cell stack and supply air to the fuel stack, a thermoelectric cooling means disposed in the case, and configured to cool the storage space, a battery charged by the fuel cell stack, and configured to supply power to the thermoelectric cooling means, and a controller configured to control the fuel cell stack and the thermoelectric cooling means.