The use of bulk effective masses in simulations of the modern-day ultra-scaled transistor is erroneous due to the strong dependence of the band structure on the cross-section dimensions and shape. This has to be accounted for in transport simulations due to the significant impact of the effective masses on quantum confinement effects and mobility. In this article, we present a methodology for the extraction of the electron effective masses, in both confinement and the transport directions, from the simulated electronic band structure of the nanowire channel. This methodology has been implemented in our in-house three-dimensional (3D) simulation engine, NESS (Nano-Electronic Simulation Software). We provide comprehensive data for the effective masses of the silicon-based nanowire transistors (NWTs) with technologically relevant cross-sectional area and transport orientations. We demonstrate the importance of the correct effective masses by showing its impact on mobility and transfer characteristics. © 2019 by the authors.