A fuel cell system having a fuel cell including at least one cell with an electrolyte membrane, the fuel cell system comprising: an index value acquirer configured to obtain a temperature index value correlated to temperature of a short circuit area in each cell; and a controller configured to control a control parameter of the fuel cell affecting the temperature of the short circuit area, such that the temperature index value is within a predetermined range set to make the temperature of the short circuit area lower than a decomposition temperature of the electrolyte membrane to keep the fuel cell generating, characterized by a resistance value acquirer configured to obtain a resistance value of the short circuit area, wherein the controller sets the predetermined range of the temperature index value, based on the resistance value of the short circuit area, the temperature index value is a voltage value of each cell, and the controller determines whether a voltage value at low load of each cell, which is a voltage value of each cell at a specified low load, is reduced from an initial value, makes a comparison between a first characteristic, which is an I-V characteristic of a first cell having reduced voltage at low load from the initial value, and a second characteristic, which is an I-V characteristic having unchanged voltage at low load from the initial value, controls the resistance value acquirer to reacquire the resistance value of the short circuit area when there is a reduction of a corrected voltage value at low load from the initial value in the first characteristic, which is corrected based on a difference in voltage value of each cell between the first characteristic and the second characteristic at a specified high load, and updates the predetermined range based on the reacquired resistance value of the short circuit area. an index value acquirer configured to obtain a temperature index value correlated to temperature of a short circuit area in each cell; and a controller configured to control a control parameter of the fuel cell affecting the temperature of the short circuit area, such that the temperature index value is within a predetermined range set to make the temperature of the short circuit area lower than a decomposition temperature of the electrolyte membrane to keep the fuel cell generating, characterized by a resistance value acquirer configured to obtain a resistance value of the short circuit area, wherein the controller sets the predetermined range of the temperature index value, based on the resistance value of the short circuit area, the temperature index value is a voltage value of each cell, and the controller determines whether a voltage value at low load of each cell, which is a voltage value of each cell at a specified low load, is reduced from an initial value, makes a comparison between a first characteristic, which is an I-V characteristic of a first cell having reduced voltage at low load from the initial value, and a second characteristic, which is an I-V characteristic having unchanged voltage at low load from the initial value, controls the resistance value acquirer to reacquire the resistance value of the short circuit area when there is a reduction of a corrected voltage value at low load from the initial value in the first characteristic, which is corrected based on a difference in voltage value of each cell between the first characteristic and the second characteristic at a specified high load, and updates the predetermined range based on the reacquired resistance value of the short circuit area.