A system and method for diagnosing a fuel cell stack are provided. The method includes determining, by a controller, a time at which diagnosing the fuel cell stack is required based on a plurality of factors and driving a motor adjusted to a first efficiency value for a predetermined first reference time period based on the diagnosis determination. In addition, the controller is configured to drive the motor adjusted to a second efficiency value when the first reference time period has elapsed. A state of the fuel cell stack is then diagnosed based on a voltage variance of the fuel cell stack between driving the motor adjusted to the first efficiency value and second efficiency value.