This study reviews the application of velocity-encoded magnetic resonance imaging (MRI) for the calculation of wall shear stress (WSS). The basics of velocity-encoded MRI and WSS are reviewed and calculation methods for estimation of the WSS from 2D or 3D (cine) velocity-encoded MRI data are presented. In recent years, there has been a trend towards 3D WSS quantification methods. Current clinical applications of WSS are discussed, including an overview of estimated WSS magnitudes in different patient groups at multiple anatomical locations (aorta, carotid arteries, and intracranial aneurysms). A large variation was found between different WSS calculation methods. The future of MRI-based WSS calculations depends on its prognostic and diagnostic value, both of which need to be further explored in clinical studies. In this context, both further improvement of the quality of velocity-encoded MRI data and scan time reduction are pivotal.