A fuel cell system includes a first heating structure that increases an internal temperature of the stack by passing exhaust gas of the process burner through the stack; and a second heating structure that increases the internal temperature of the stack by passing heated cooling water through the stack after the cooling water is heated by heat exchange with the exhaust gas of the process burner. Accordingly, when rapid heating of a stack is necessary like during a start up operation, a time required for the fuel cell system to reach a normal operation can be greatly reduced since the stack can be simultaneously heated using high temperature exhaust gas and heated cooling water.