The syntectonic continental conglomerates of the South-Central Pyrenees record the late stages of thin-skinned transport of the South-Pyrenean Central Units and the onset of exhumation of the Pyrenean Axial Zone (AZ) in the core of the orogen. New magnetostratigraphic data of these syntectonic continental conglomerates have established their age as Late Lutetian to Late Oligocene. The data reveal that these materials were deposited during intense periods of tectonic activity of the Pyrenean chain and not during the cessation of the deformation as considered previously. The magnetostratigraphic ages have been combined with new detrital apatite fission track (AFT) thermochronology from AZ-derived granite cobbles within the syntectonic conglomerates. Distribution of the granitic cobbles with different AFT ages and track lengths combined with their depositional ages reveal information on the timing and rate of episodes of exhumation in the orogen. Some AFT ages are considerably older than the AFT ages of the outcropping AZ granitic massifs, indicating erosion from higher crustal levels within the massifs than presently exposed or from completely eroded plutons. Inverse thermal modelling reveals two well-defined periods of rapid cooling in the hinterland at ca. 50–40 and ca. 30–25 Ma, with another poorly defined cooling episode at ca. 70–60 Ma. The lowest stratigraphic samples experienced postburial annealing caused by the deposition of younger syntectonic sediments during progressive burial of the south Pyrenean thrust and fold belt. Moreover, samples from the deeper stratigraphic levels also reveal postorogenic cooling during the Late Miocene as a response to the excavation of the Ebro River towards the Mediterranean Sea. Our data strongly support previous ideas about the burial of the South Pyrenean fold and thrust belt by Late Palaeogene syntectonic conglomerates and their subsequent re-excavation and are consistent with other thermochronological data and thermal modelling from the interior part of the orogen.