An air-breathing-type polymer electrolyte membrane fuel cell and an operating method thereof capable of being stably started and operated by controlling an output current and temperature of a fuel cell stack in a predetermined range is controlled in a predetermined range so that the initial driving time of the system can be shortened through the high current operation in the low output state. The operating method of the air-breathing-type polymer electrolyte membrane fuel cell includes the steps of detecting an output current of a fuel cell stack; comparing a maximum reference value and a minimum reference value of the detected output current; and keeping the output current below the maximum reference value and above the minimum reference value.