Apatite fission-track (AFT) dating applied to uplifted Variscan basement blocks of the Bavarian Forest is employed to unravel the low-temperature history of this segment of the Bohemian Massif. Twenty samples were dated and confined track lengths of four samples were measured. Most samples define Cretaceous APT ages between 110 and 82 Ma (Albian to Campanian) and three samples give older ~148–140 Ma (Jurassic–Cretaceous boundary) ages. No discernible regional age variations exist between the areas north-east and south-west of the Pfahl shear zone, but >500 m post-Jurassic and post-Cretaceous vertical offsets along this and other faults can be inferred from elevation profile analyses. The AFT ages clearly postdate the Variscan exhumation history of the Bavarian Forest. Thermal modeling reveals that the ages are best explained by a slight reheating of the basement rocks to temperatures within the apatite partial annealing zone during the middle and late Jurassic and/or by late Cretaceous marine transgression causing burial heating, which affected marginal low-lying areas of the Bohemian Massif and the Bavarian Forest. Late Jurassic period was followed by enhanced cooling through the 120–60 °C temperature interval during the subsequent exhumation phase for which denudation rates of ~100 m myr−1 were calculated. On a regional scale, Jurassic–Cretaceous AFT ages are ubiquitous in marginal structural blocks of the Bohemian Massif and seem to reflect the exhumation of these zones more distinctly compared to central parts.