The central Pyrenees experienced an episode of rapid exhumation in Late Eocene–Early Oligocene times. Erosional products shed from the range during this time were deposited in large palaeovalleys of the southern flank of the Axial Zone, leading to significant sediment accumulation. A recent numerical modelling study of the post-orogenic exhumation and relief history of the central Axial Zone allowed us to constrain this valley-filling episode in terms of timing and thickness of conglomeratic deposits. This paper aims to test these results for the southern fold-and-thrust belt using apatite fission-track and (U–Th)/He analysis on detrital samples from the Tremp–Graus and Ager basins. Inverse thermal-history modelling of the low-temperature thermochronology data indicates that the fold-and-thrust belt was covered during the Late Eocene to Miocene by 0.7–1.6 km of sediments and confirms the timing of re-excavation of the valleys during the Miocene. A detailed analysis of the apatite (U–Th)/He results shows that the significant scatter in grain ages can be explained by the influence of alpha-recoil damage with varying effective uranium content together with distinct pre-depositional thermal histories; the age scatter is consistent with initial exhumation of the sediment sources during the Triassic and Early Cretaceous.