We calculate the present-day lithospheric strength of the Eastern Alps along the new reflection seismic profile TRANSALP to examine vertical and lateral strength variations and their implications on neotectonic activity of the Eastern Alps. The large-scale geometry of the Eastern Alps and the spatial distribution of upper, and lower crustal layers, and the lithospheric mantle is constrained by the deep seismic line. Two rheological models, coupled to a kinematic thermal model that accounts for the thermal evolution of the Eastern Alps for the last 30 Myr, are investigated for the present-day lithospheric configuration in the Eastern Alps. Models with strong (Model A) and weak (Model B) crustal rheologies predict the European and the Adriatic plates to be stronger than the central zone of the orogen comprising the region between the Inntal Fault and the Periadriatic Fault. Model A is characterized by a brittle-ductile boundary between 14 and 9 km depth and strong coupling of the mechanically strong lower crust to the upper mantle, whereas Model B suggests the presence of a thick decoupling zone between the upper crust and the upper mantle and a shallower brittle-ductile boundary (7–10 km). Of these end-member scenarios, Model A is in better agreement with neotectonic data including seismicity down to the upper-lower crust boundary within the Adriatic plate, uplift of the central zone of the Eastern Alps and the Southern Alps, and eastward escape of fault-bound blocks. Such deformation pattern is best explained by lateral extrusion upon north-south compression supporting a strong-weak-strong configuration of tectonic units along the TRANSALP line.