The Brenner Base Tunnel cuts almost the entire nappe stack within the Eastern Alps. From N to S, it pierces Upper Austroalpine nappes, the Tauern Window dome (Sub-Penninic, Europe derived core, enveloped by oceanic Penninic nappes), the southern continuation of the Austroalpine realm, the Periadriatic Mauls tonalitic lamellae and the Southalpine Brixen Granite. A transect near Mauls (South Tyrol), comprising the latter three units and the Pustertal fault were sampled during excavation. Time-temperature simulation and linear inversion were applied to low temperature thermochronology ages from fission track (apatite and zircon) and (U-Th)/He in apatite analysis. Results indicate (i) young, Miocene to (at least) Pliocene uplift north of the Pustertal fault, (ii) the position of the southern border of Alpine metamorphism within the narrow, overtilted Austroalpine nappe stack, attributed to the Defereggen-Antholz-Vals fault zone, (iii) most striking differential vertical movement during the Miocene Giudicarie phase between 17 and 8 Ma. These findings match with the patterns described in a regional exhumation study, based on compiled thermochronologic ages for the Austroalpine domain south of the Tauern Window and with structural observations. Time step plots of exhumation rates unravel (i) a clearly decoupled Miocene exhumation history of Alpine metamorphic and Alpine non-metamorphic units until 8Ma, (ii) a significant pre-Miocene E-W trend towards the most recent cooling ages in the Mauls area for Alpine metamorphic units and (iii) an E-W decoupling of Alpine non-metamorphic units at the Eisack Valley from 17 Ma onwards during the Giudicarie phase.