Detrital apatite fission-track (AFT) thermochronology has been applied to lower Pleistocene lacustrine fan-delta sediments of the NE shoulder of the Mugello Basin, the youngest and closest to the main watershed among the Northern Apennines intermontane basins. The aim was to decode the shoulder uplift dynamics during the development of the basin through the analysis of the Quaternary fluvio-lacustrine deposits. Bedrock shoulder analysis, performed to match the detrital AFT data with their source, revealed the presence of a unexpected only partially annealed portion of a turbidite foredeep unit (AFT ages >7–5 Ma) belonging to the structural complex that constitutes the shoulder bedrock. These data disagree with the AFT age distribution pattern of the well-studied Northern Apennines chain, suggesting a segmentation of the foredeep basin. The latter may have been related to the presence of a tectonically induced topographic high (pre-late Langhian) in the area limiting the thickness of the overriding Ligurian lid. On the other hand, detrital AFT data provided arguments for understanding the dynamics of Mugello Basin shoulder uplift and rotation. The proportion in the different stratigraphic units of the fan-delta sediments of single grains showing young (reset) and old (non-reset) ages points to late Early Pleistocene timing of the development of the SW-verging backthrust that characterizes the study area. These data confirm and detail the picture of an early Quaternary development of the Mugello Basin under a compressional setting, only later (middle Pleistocene to present) superimposed by normal faultings.