Second harmonic generation using nonlinear ultrasonic waves have been shown to be an early indicator of possible fatigue damage in nuclear power plant components. This technique relies on measuring amplitudes, making it highly susceptible to variations in transducer coupling and instrumentation. This paper proposes an experimental procedure for in-situ surface wave nonlinear ultrasound measurements on specimen with permanently mounted transducers under high cycle fatigue loading without interrupting the experiment. It allows continuous monitoring and minimizes variation due to transducer coupling. Moreover, relations describing the effects of the measurement system nonlinearity including the effects of the material transfer function on the measured nonlinearity parameter are derived. An in-situ high cycle fatigue test was conducted using two 304 stainless steel specimens with two different excitation frequencies. A comprehensive analysis of the nonlinear sources, which result in variations in the measured nonlinearity parameters, was performed and the effects of the system nonlinearities are explained and identified. In both specimens, monotonic trend was observed in nonlinear parameter when the value of fundamental amplitude was not changing.