A modern system theory based nonlinear control design is discussed in this paper for successful operation of an air-breathing engine operating at supersonic speed. The primary objective of the control design of such an air-breathing engine is to ensure that the engine dynamically produces the thrust that tracks a commanded value of thrust as closely as possible by regulating the fuel flow to the combustion system. However, since the engine operates in the supersonic range, an important secondary objective is to manage the shock wave configuration in the intake section of the engine which is manipulated by varying the throat area of the nozzle. A nonlinear sliding mode control technique has been successfully used to achieve both of the above objectives. In this problem, since the process is faster than the actuators, independent control designs are also carried out for the actuators as well to assure the satisfactory performance of the system. Moreover, to filter out the sensor and process noises and to estimate the states for making the control design operate based on output feedback, an extended Kalman Filter based state estimation design is also carried out. The promising simulation results suggest that the proposed control design approach is quite successful in obtaining robust performance of the air-breathing engine.