The transition area between the Pannonian Basin and the East Carpathians is the subject of considerable tectonic research in Central Europe because of its geological diversity, especially for Lithosphere–Asthenosphere Boundary determinations. The major objective of this study is to investigate the Earth’s lithospheric structure and in particular to determine the Lithosphere–Asthenosphere Boundary from the Pannonian Basin, through the Transylvanian Basin to the Carpathian Bend area. We recorded six new deep magnetotelluric soundings and used two archive measurements to complete the information and to put additional constraints on the depth of the Lithosphere–Asthenosphere Boundary. In the part of the discussions we provide a brief overview of the existing various methodologies and Lithosphere–Asthenosphere Boundary determinations for the wider Carpathian–Pannonian region and Europe and comparison with new magnetotelluric results. The lowest Lithosphere–Asthenosphere Boundary depth was detected in the Pannonian Basin (~50 km). Our results indicate in addition that the Lithosphere-Asthenosphere Boundary beneath the Transylvanian Basin (~70–80 km) is not thick and much thinner than those of the European and Moesian Platforms. The additional geophysical information (geomagnetic data and phase tensor results) detected the presence of deep well conductive zones towards the Pannonian Basin, the Bogdan Vodă–Dragoș Vodă fault and the East Carpathians. This could be explained by the elevated position of the well conductive asthenosphere in the Pannonian Basin and deep and presumably fluid rich tectonic zones associated with the Bogdan Vodă–Dragoș Vodă fault and the East Carpathians. The phase tensors highlighted that the most complex tectonic zones are present in the vicinity of the East Carpathians (where the average Lithosphere–Asthenosphere Boundary depth is >100 km), which is in line with the relatively young age of the mountain belt and the very complex nature of collisional orogens.