The implant of self‐expandable Ni‐Ti stents for the treatment of peripheral diseases has become an established medical practice. However, the reported failure in clinics highlights the open issue of the fatigue characterization of these devices. One of the most common approaches for calculating the Ni‐Ti fatigue limit (commonly defined in terms of mean and alternate strain for a fixed number of cycles) consists of using surrogate specimens which replicate the strain distributions of the final device but in simplified geometries. The main drawback lies in the need for computational models to determine the local distribution and, hence, interpret the experimental results. This study aims at investigating the role of different choices in the model preparation, such as the mesh refinement and the element formulation, on the output of the fatigue analysis. The analyses show a strong dependency of the numerical results on modeling choices. The use of linear reduced elements enriched by a layer of membrane elements is successful to increase the accuracy of the results, especially when coarser meshes are used. Due to material nonlinearity and stent complex geometries, for the same loading conditions and element type, (i) different meshes result in different couples of mean and amplitude strains and (ii) for the same mesh, the position of the maximum mean strain is not coincident with the maximum amplitude, making difficult the selection of the limit values.