A fuel cell system comprising: a plurality of fuel cell stacks connected in series; a refrigerant distribution passage; and a controller, characterized in that the fuel cell stacks are constituted by first fuel cell stacks (12-k) of m units and second fuel cell stacks (12-z) of n-m units, a refrigerant is individually distributed to the plurality of the fuel cell stacks through said refrigerant distribution passage; by a pre-distribution refrigerant flow rate acquiring unit configured to acquire a pre-distribution refrigerant flow rate (q air) that is a flow rate of the refrigerant before distribution; first outlet temperature (T o1[k]) detecting units (54-k) that are provided at a refrigerant outlets of the first fuel cell stacks (12-k) and are configured to detect a first outlet temperature (T o1[k]) that is a refrigerant outlet temperature of the respective ones of the first fuel cell stacks (12-k); voltage acquiring units (56-k) configured to acquire a first voltage (V 1[k]) that is a voltage of respective ones of the first fuel cell stacks (12-k); a current acquiring unit configured to acquire a first current that is a current of the first fuel cell stacks (12-k); and in that the controller is programmed to calculate: a first calorific value (Q gen1[k]) of the each of the first fuel cell stacks (12-k) from a theoretical electromotive force E 0 of each of the first fuel cell stacks (12-k), the first voltage (V 1[k]), and the first current using an equation below: Q gen 1 k = I E 0 − V 1 k, where k is an integer from 1 to m, a first individual supply flow rate (q air_d[k]) from the first calorific value (Q gen1[k]) of the each of the first fuel cell stacks (12-k), the pre-distribution refrigerant flow rate (q air), the first voltage (V 1[k]), the first current, the first outlet temperature (T o1[k]), and an assumed first outlet temperature value (T O1exp[k]) which is a theoretical value of an outlet air temperature expected to be detected at the first fuel cell stacks (12-k) if a uniform flow rate of air is distributed to the first fuel cell stacks (12-k), using an equation below: q air 1 _ d k = q air n ⋅ Q gen 1 k Q gen 1 k + q air n ⋅ C air T O 1 k − T O 1 exp k and a second individual supply flow rate (q air2_d[z]) that is a flow rate of the refrigerant individually supplied to the second fuel cell stacks (12-z) from the first individual supply flow rates (q air1_d[k]) and the pre-distribution refrigerant flow rate (q air) using an equation below: q air 2 _ d z = q air − q air 1 _ d 1 + q air 1 _ d 2 + ⋅ ⋅ ⋅ ⋅ ⋅ + q air 1 _ d m n − m where z is an integer from n-m to n so as to individually distribute the refrigerant to each fuel cell with the respective calculated individual supply flow rate. a plurality of fuel cell stacks connected in series; a refrigerant distribution passage; and a controller, characterized in that the fuel cell stacks are constituted by first fuel cell stacks (12-k) of m units and second fuel cell stacks (12-z) of n-m units, a refrigerant is individually distributed to the plurality of the fuel cell stacks through said refrigerant distribution passage; by a pre-distribution refrigerant flow rate acquiring unit configured to acquire a pre-distribution refrigerant flow rate (q air) that is a flow rate of the refrigerant before distribution; first outlet temperature (T o1[k]) detecting units (54-k) that are provided at a refrigerant outlets of the first fuel cell stacks (12-k) and are configured to detect a first outlet temperature (T o1[k]) that is a refrigerant outlet temperature of the respective ones of the first fuel cell stacks (12-k); voltage acquiring units (56-k) configured to acquire a first voltage (V 1[k]) that is a voltage of respective ones of the first fuel cell stacks (12-k); a current acquiring unit configured to acquire a first current that is a current of the first fuel cell stacks (12-k); and in that the controller is programmed to calculate: a first calorific value (Q gen1[k]) of the each of the first fuel cell stacks (12-k) from a theoretical electromotive force E 0 of each of the first fuel cell stacks (12-k), the first voltage (V 1[k]), and the first current using an equation below: Q gen 1 k = I E 0 − V 1 k, where k is an integer from 1 to m, a first individual supply flow rate (q air_d[k]) from the first calorific value (Q gen1[k]) of the each of the first fuel cell stacks (12-k), the pre-distribution refrigerant flow rate (q air), the first voltage (V 1[k]), the first current, the first outlet temperature (T o1[k]), and an assumed first outlet temperature value (T O1exp[k]) which is a theoretical value of an outlet air temperature expected to be detected at the first fuel cell stacks (12-k) if a uniform flow rate of air is distributed to the first fuel cell stacks (12-k), using an equation below: q air 1 _ d k = q air n ⋅ Q gen 1 k Q gen 1 k + q air n ⋅ C air T O 1 k − T O 1 exp k and a second individual supply flow rate (q air2_d[z]) that is a flow rate of the refrigerant individually supplied to the second fuel cell stacks (12-z) from the first individual supply flow rates (q air1_d[k]) and the pre-distribution refrigerant flow rate (q air) using an equation below: q air 2 _ d z = q air − q air 1 _ d 1 + q air 1 _ d 2 + ⋅ ⋅ ⋅ ⋅ ⋅ + q air 1 _ d m n − m where z is an integer from n-m to n so as to individually distribute the refrigerant to each fuel cell with the respective calculated individual supply flow rate.