The large number and distribution of rollback systems in Mediterranean orogens infer the possibility of interacting extensional back-arc deformation driven by different slabs. The formation of the Pannonian back-arc basin is generally related to the rapid Miocene rollback of a slab attached to the European continent. A key area of the entire system that is neglected by kinematic studies is the connection between the South Carpathians and Dinarides. In order to derive an evolutionary model, we interpreted regional seismic lines traversing the entire Serbian part of the Pannonian Basin. The observed deformation is dominantly expressed by the formation of Miocene extensional detachments and (half) grabens. The extensional geometries and associated synkinematic sedimentation that migrated in time and space allow the definition of a continuous and essentially asymmetric early to late Miocene extensional evolution. This evolution was followed by the formation of few uplifted areas during the subsequent latest Miocene–Quaternary inversion. The present-day extensional geometry changing the strike across the basin is an effect of the clockwise rotation of the South Carpathians and Apuseni Mountains in respect to the Dinarides. Our study infers that the Carpathian rollback is not the only mechanism responsible for the formation of the Pannonian Basin; an additional middle Miocene rollback of a Dinaridic slab is required to explain the observed structures. Furthermore, the study provides constraints for the pre-Neogene orogenic evolution of this junction zone, including the affinity of major crustal blocks, obducted ophiolitic sequences and the Sava suture zone.