Resolving the Mesozoic and Cenozoic palaeogeography and geomorphologic development of outcropping Variscan basement is a pre-condition for the understanding of central European geodynamics. For our study, we have applied apatite fission-track (AFT) and apatite (U–Th)/He (AHe) thermochronology to surface rocks of the southeastern Bohemian Massif. 46 samples were examined by the AFT method. Additional AHe dating was applied to 8 of them. The AFT ages range from 251 ± 46 to 60.2 ± 4.8 Ma. AHe ages range from 25 to 525 Ma with rather high intra-sample scatter. On a regional scale, the AFT ages generally decrease from mainly late Variscan in the NE to Late Cretaceous and Paleocene in the SW. This regional age asymmetry relative to the NW–SE trending watershed of the Weinsberg Forest is neither compatible with regional uplift of a single block nor with large-scale lithospheric updoming. The lack of age breaks along late Variscan faults demonstrates that strong vertical offset cannot have occurred in Cretaceous and Cenozoic times. Inverse modeling of thermochronological data indicates regional Early Cretaceous cooling and subsequent reheating during the Late Cretaceous. Rocks of the present-day surface were heated up to a temperature of ca. 80 °C without full reset of the AFT system. This thermal history is compatible with the existence of a large mainland in Early Cretaceous times and a subsequent sedimentary reburial until the Campanian on the order of up to 1 km overburden. Parts of the exhumed weathering basal relief to the N and NE of the Weinsberg Forest are inherited as ‘sealed relief’ from Middle Cretaceous time. The observed regional asymmetry of AFT data is best explained by the development of a continental escarpment adjacent to the North Penninic Ocean in latest Cretaceous to Paleogene times. A final episode of accelerated cooling after ca. 20 Ma, as indicated by thermochronological modeling, is tentatively ascribed to either collisional coupling of the Alpine-Carpathian nappe pile with its northern foreland or to East-Alpine slab detachment.