In a low‐seismicity context, the use of numerical simulations becomes essential due to the lack of representative earthquakes for empirical approaches. The goals of the EUROSEISTEST Verification and Validation Project (E2VP) are to provide (1) a quantitative analysis of accuracy of the current, most advanced numerical methods applied to realistic 3D models of sedimentary basins (verification) and (2) a quantitative comparison of the recorded ground motions with their numerical predictions (validation). The target is the EUROSEISTEST site located within the Mygdonian basin, Greece. The site is instrumented with surface and borehole accelerometers, and a 3D model of the medium is available. The simulations are performed up to 4 Hz, beyond the 0.7 Hz fundamental frequency, thus covering a frequency range at which ground motion undergoes significant amplification. The discrete representation of material heterogeneities, the attenuation model, the approximation of the free surface, and nonreflecting boundaries are identified as the main sources of differences among the numerical predictions. The predictions well reproduce some, but not all, features of the actual site effect. The differences between real and predicted ground motions have multiple origins: the accuracy of source parameters (location, hypocentral depth, and focal mechanism), the uncertainties in the description of the geological medium (damping, internal sediment layering structure, and shape of the sediment‐basement interface). Overall, the agreement reached among synthetics up to 4 Hz despite the complexity of the basin model, with code‐to‐code differences much smaller than predictions‐to‐observations differences, makes it possible to include the numerical simulations in site‐specific analysis in the 3D linear case and low‐to‐intermediate frequency range.