Control of small turbojet engines is challenging due to the small number of sensors and actuators. In these engines, typically the spool speed and exhaust gas temperature are the measured variables and the fuel flow is the only manipulated variable. However, the thrust command must be achieved and the engine’s structural and operational limitations must be safeguarded. In this research, a minimum selector control structure with a saturation function is presented for controlling small turbojet engines. One control loop is considered to control the spool speed and another loop is used to manage the exhaust gas temperature. The output of the control loops is the fuel flow rate and the minimum value is selected between them. To prevent the compressor surge and combustor blow-out during engine acceleration/deceleration, a fuel flow rate saturation is defined. Due to the switching structure of the proposed controller and existence of the saturation function, stability analysis is a critical issue. Therefore, a methodology is presented to analyse the stability of the proposed structure. In simulation study, a nonlinear thermodynamic model that matches more than 90% with the test data is used and the response of the proposed controller is compared with a proportional integral (PI) controller. In a comprehensive scenario, the throttle degree varies from 75% to 100%. Using the PI controller, some outputs have some overshoot and the exhaust gas temperature exceeds the corresponding constraint by 40K. While the proposed minimum selector controller, in addition to accurately fulfilling the thrust command, fully protects the limitations governing engine variables.