18 samples were collected during two field trips in 2022 and 2023 to Italy and Austria to determine the late Cenozoic exhumation history of three valleys (Ahrntal, Floitental, Krimmler Achental) in the glacially overprinted Tauern Window. This dataset contains single-grain corrected and uncorrected (U-Th)/He apatite ages ranging from 1.4 Ma to 14.3 Ma alongside Uranium, Thorium, Samarium, and Helium concentrations, Ft correction, grain size, weighted errors, and sample location information. Apatites were separated at the University of Potsdam Mineral Separation Lab by first crushing, then separating minerals by density on a Wilfley shake table, by magnetic components of a Franz, and by density using heavy liquids sodium polytungstate and diiodomethane. Single apatite grains were carefully hand-picked under a microscope (Leica) and packed in Pt tubes. At the University of Potsdam Thermochronology Lab, single-grain aliquots were heated until full degassing using an Alphachron (Australian Scientific Instruments), and (He) gas concentrations measured using a quadrupole mass spectrometer. Parent isotope concentrations were determined at the ElMiE-Lab at the GFZ Helmholz Centre for Geosciences in Potsdam, Germany. Quantification of isotope concentration was done after He extraction by complete dissolution of the sample, spiking with a calibrated U-Th-Sm spike. Dissolution of the sample was achieved by digestion using ultra pure HF, HCl and HNO3 in a pressure vessel for several days. Isotope analysis was performed on a sector field ICP-MS (Element XR, Thermo Fischer). Between each individual analysis all systems were cleaned and blanks were run. All sample components (hand specimens, separates, crystal grains) are stored at the Institute of Geosciences, University of Potsdam, Germany.