A control system and method controls an output of a fuel cell. A fuel cell stack controller that receives an output request signal and that generates an oxidant request signal and a fuel request signal using a first inverse model. A fuel delivery controller receives the fuel request signal, generates a fuel command using a second inverse model and generates a delivered fuel signal using a first model. An oxidant delivery controller receives the oxidant request signal, generates an oxidant command using a third inverse model and generates a delivered oxidant signal using a second model. The fuel cell stack controller receives the delivered oxidant signal from the second model and the delivered fuel signal from the first model and calculates a power available signal using a third model.