The Vienna Basin is a tectonically complex Neogene basin situated at the Alpine–Carpathian transition. This study analyzes a detailed quantification of subsidence in the northern and central parts of the Vienna Basin to understand its tectonic subsidence evolution. About 200 wells were used to arrange stratigraphic setting, and wells reaching the pre-Neogene basement were analyzed for subsidence. To enhance the understanding of the regional subsidences, the wells were sorted into ten groups based on their position on major fault blocks. In the Early Miocene, subsidence was slow and along E–W to NE–SW trending axis, indicating the development of thrust-controlled piggyback basins. During the late Early Miocene data show abruptly increasing subsidence, making the initiation of the Vienna pull-apart basin system. From the Middle Miocene, the tectonic subsidence curves show regionally different patterns. The tectonic subsidence during the Middle Miocene varies laterally across the Vienna Basin, and the differential subsidence can be related to the changing tensional regime of weakening transtension and strengthening extension toward the late Middle Miocene. From the late Middle Miocene to the Late Miocene, the tectonic subsidence occurred dominantly along the regional active faults, and corresponds to the axis of E–W trending extension of the western parts of the Pannonian Basin system. In the Quaternary the Vienna Basin has been reactivated, and resulted in subsidence along the NE–SW trending Vienna Basin transfer fault system.