An extensive low-temperature thermochronology study of the Swiss part of the North Alpine Foreland Basin has been conducted with the aim of deciphering the late Neogene basin development. Apatite fission-track (AFT) ages from wells located in the distal and weakly deformed Plateau Molasse reveal rapid, km-scale erosion with an onset in early Pliocene times. The distribution of erosion implies that there was a strong gradient in late Miocene deposition rates along the strike of the basin, with an increase towards the northeast. Additionally, renewed tectonic activity and km-scale out-of-sequence thrusting during Plio-Pleistocene times is indicated by AFT data from wells within the thrusted, proximal Subalpine Molasse. Several different mechanisms driving late Neogene basin erosion and accelerated erosional discharge from the European Alps have been considered in the literature. Based on our AFT results, we reevaluate previously published hypotheses, and suggest that a change in climate and/or drainage reorganisation coincided and possibly interacted with preexisting tectonic and geodynamic forces in the Alpine region.