A method of operating a fuel cell cogeneration system comprises the steps of cooling a fuel cell by circulating an internal heat transfer medium through the fuel cell while the fuel cell is generating electric power, storing an external heat transfer medium in a heat utilization portion, detecting remaining calories of the heat utilization portion by a first detector provided at the heat utilization portion, increasing a temperature of the fuel cell to an operating temperature by carrying out a first temperature increasing operation, and increasing the temperature of the fuel cell to the operating temperature by carrying out a second temperature increasing operation.