In recent years, the nonlinear ultrasonic technique has been widely utilized for detecting fatigue crack, one of the most common forms of damage. However, one of limitations associated with this technique is that nonlinearities can be produced not only by damage but also by various intrinsic effects such as boundary conditions. The objective of this paper is to demonstrate the application of a nonlinear ultrasonic subharmonic method for detecting fatigue cracks with nonlinear boundary conditions. The fatigue crack was qualitatively modeled as two elastic, frictionless half spaces that enter into contact during vibration and where the contact obeys the basic Hertz contact law. The nonlinear ordinary differential equation drawn from the developed model was solved with the method of multiple scales. The threshold of subharmonic generation was studied. Different threshold behaviors between the nonlinear boundary condition and the fatigue crack were found that can be used to distinguish the source of nonlinear subharmonic features. To evaluate the proposed method, experiments using an aluminum plate with a fatigue crack were conducted to quantitatively verify the subharmonic resonance range. Two surface-bonded piezoelectric transducers were used to generate and receive ultrasonic wave signals. The experimental results demonstrated that the subharmonic component of the sensing signal could be used to detect the fatigue crack and further to distinguish it from inherent nonlinear boundary conditions.