A fuel cell system comprising: a fuel cell stack formed by stacking a plurality of unit cells horizontally and having, in the stacked body, manifolds through which to supply and discharge reaction gases to and from each of the unit cells; drainage paths (1A, 1B) extending from an anode-off-gas discharge manifold, on both end sides of the fuel cell stack in a stacking direction of the unit cells, respectively; liquid-water buffers (6A, 6B) provided in the drainage paths (1A, 1B) on both end sides and designed to hold resultant water at positions upstream of outlet ports to an outside, respectively; control valves (7A, 7B) which open and close the outlet ports to the outside, provided in the drainage paths (1A, 1B) on both end sides, respectively; an off-gas flow path which communicates with at least one of the drainage paths (1A, 1B) on both end sides; and a purge valve which discharges an impurity gas from the off-gas flow path, wherein the two control valves (7A, 7B) are configured to be opened for a required drainage time (tA, tB) to drain the liquid-water buffers (6A, 6B), respectively, the required drainage time (tA, tB) being a period of time required to drain an estimated amount of the resultant water generated in the fuel cell stack through either one of the two control valves (7A, 7B), the estimated amount of the resultant water being estimated based on an operating condition of the fuel cell stack, and the purge valve is configured to be opened for a required discharge time (tC) if an amount of the impurity gas dischargeable from the two control valves (7A, 7B) while the two control valves (7A, 7B) are respectively opened for the required drainage time (tA, tB) is smaller than an estimated amount of the impurity gas generated in the fuel cell stack, the required discharge time (tC) being a period of time obtained by subtracting the required drainage time (tA, tB) from a required purge time (tN 2) that is determined from the estimated amount of the impurity gases, the estimated amount of the impurity gas being estimated based on the operating condition of the fuel cell stack. a fuel cell stack formed by stacking a plurality of unit cells horizontally and having, in the stacked body, manifolds through which to supply and discharge reaction gases to and from each of the unit cells; drainage paths (1A, 1B) extending from an anode-off-gas discharge manifold, on both end sides of the fuel cell stack in a stacking direction of the unit cells, respectively; liquid-water buffers (6A, 6B) provided in the drainage paths (1A, 1B) on both end sides and designed to hold resultant water at positions upstream of outlet ports to an outside, respectively; control valves (7A, 7B) which open and close the outlet ports to the outside, provided in the drainage paths (1A, 1B) on both end sides, respectively; an off-gas flow path which communicates with at least one of the drainage paths (1A, 1B) on both end sides; and a purge valve which discharges an impurity gas from the off-gas flow path, wherein the two control valves (7A, 7B) are configured to be opened for a required drainage time (tA, tB) to drain the liquid-water buffers (6A, 6B), respectively, the required drainage time (tA, tB) being a period of time required to drain an estimated amount of the resultant water generated in the fuel cell stack through either one of the two control valves (7A, 7B), the estimated amount of the resultant water being estimated based on an operating condition of the fuel cell stack, and the purge valve is configured to be opened for a required discharge time (tC) if an amount of the impurity gas dischargeable from the two control valves (7A, 7B) while the two control valves (7A, 7B) are respectively opened for the required drainage time (tA, tB) is smaller than an estimated amount of the impurity gas generated in the fuel cell stack, the required discharge time (tC) being a period of time obtained by subtracting the required drainage time (tA, tB) from a required purge time (tN 2) that is determined from the estimated amount of the impurity gases, the estimated amount of the impurity gas being estimated based on the operating condition of the fuel cell stack.