A fuel cell system and an operating method thereof capable of reliably reducing fuel crossover and electrolyte film deterioration is provided. A fuel cell system (100) includes: a fuel cell (104) which includes an electrolyte film (104a); aqueous solution circulation means which provides circulatory supply of aqueous methanol solution to the fuel cell (104); fuel supply means which supplies the aqueous solution circulation means with methanol fuel that has a concentration not lower than that of the aqueous methanol solution; and a main switch (152). After the main switch (152) is turned OFF, a CPU (172) controls fuel supply operation of the fuel supply means so that the amount of fuel supply to the aqueous solution circulation means is decreased. Thereafter, power generation operation of the fuel cell (104) is controlled so that the power generation is stopped, with the concentration of aqueous methanol solution lower than before the main switch (152) was turned OFF. The produced energy during shutdown is stored in a secondary battery.