In the Montes de Toledo area, located in the axial part of the Central Hercynian zone, a long-term thermo-tectonic evolution can be deduced from apatite fission-track (AFT) data in conjunction with tight geological constraints derived from the knowledge of regional geology and other independent chronometers. The area is composed of two different blocks separated by the Toledo Shear Zone (TSZ). The northern block is a granulite facies anatectic terrane. The southern block is composed of greenschist facies Paleozoic sediments intruded by a late Hercynian granitic pluton. A total of 13 samples have been recovered for AFT analysis. AFT ages in both blocks cluster around 189–221 Ma, with mean confined track lengths between 11.4 μm and 12.4 μm. Modeling of the AFT data indicates that the thermal history is broadly similar in both blocks, which constrains the main movement of the TSZ, as essentially before the Upper Permian. AFT ages in the TSZ cluster around 124–164 Ma, and the track lengths vary between 11.4 μm and 12.4 μm. These data reveal that the fault must have been affected by a later thermal overprint as AFT ages are significantly younger than those of the footwall and hangingwall blocks. This differential thermal resetting is likely related to the advection of localized hydrothermal fluids that are responsible for the widespread Pb–Zn mineralization along the TSZ. These results give an example of resetting AFT data by hydrothermal events. The long-term evolution suggests a lack of important Alpine tectonism in the Montes de Toledo block, in clear contrast to other nearby Hercynian areas such as the Sierra de Guadarrama, where the important effect of Alpine tectonism has almost totally erased the previous thermal signal in the AFT system.