Recent studies have shown the potential for nanocrystalline metals to possess excellent fatigue resistance compared to their coarse-grained counterparts. Although the mechanical properties of nanocrystalline metals are believed to be particularly susceptible to material defects, a systematic study of the effects of geometric discontinuities on their fatigue performance has not yet been performed. In the present work, nanocrystalline Ni–40 wt%Fe containing both intrinsic and extrinsic defects were tested in tension–tension fatigue. The defects were found to dramatically reduce the fatigue resistance, which was attributed to the relatively high notch sensitivity in the nanocrystalline material. Microstructural analysis within the crack-initiation zones underneath the defects revealed cyclically-induced abnormal grain growth (AGG) as a predominant deformation and crack initiation mechanism during high-cycle fatigue. The onset of AGG and the ensuing fracture is likely accelerated by the stress concentrations, resulting in the reduced fatigue resistance compared to the relatively defect-free counterparts.