The Eger Rift is an active element of the European Cenozoic Rift System associated with intense Cenozoic intraplate alkaline volcanism and system of sedimentary basins. The intracontinental Cheb Basin at its western part displays geodynamic activity with fluid emanations, persistent seismicity, Cenozoic volcanism, and neotectonic crustal movements at the intersections of major intraplate faults. In this paper, we study detailed geometry of the crust/mantle boundary and its possible origin in the western Eger Rift. We review existing seismic and seismological studies, provide new interpretation of the reflection profile 9HR, and supplement it by new results from local seismicity. We identify significant lateral variations of the high-velocity lower crust and relate them to the distribution and chemical status of mantle-derived fluids and to xenolith studies from corresponding depths. New interpretation based on combined seismic and isotope study points to a local-scale magmatic emplacement at the base of the continental crust within a new rift environment. This concept of magmatic underplating is supported by detecting two types of the lower crust: a high-velocity lower crust with pronounced reflectivity and a high-velocity reflection-free lower crust. The character of the underplated material enables to differentiate timing and tectonic setting of two episodes with different times of origin of underplating events. The lower crust with high reflectivity evidences magmatic underplating west of the Eger Rift of the Late Variscan age. The reflection-free lower crust together with a strong reflector at its top at depths of ~28–30 km forms a magma body indicating magmatic underplating of the late Cenozoic (middle and upper Miocene) to recent. Spatial and temporal relations to recent geodynamic processes suggest active magmatic underplating in the intracontinental setting.