Provided is an apparatus for soft-sensing a fuel cell system. The apparatus includes: a connecting unit detachable from a control unit for being connected to an outside of a stationary fuel cell system; a collecting unit connected to the connecting unit and receiving data of the stationary fuel cell system; a quality variable predicting unit connected to the collecting unit and predicting a quality variable of the stationary fuel cell system based on the received data; and a monitoring unit connected to the quality variable predicting unit and outputting the predicted quality variable. The quality variable predicting unit is configured to predict the quality variable predictable including at least any one of a concentration of carbon monoxide in a reformed gas at a rear end of a fuel converting system, and a concentration of methane in the reformed gas at the rear end of the fuel converting system.