The central parts of the Sredna Gora Zone in Bulgaria have experienced a complex Alpine tectonic evolution. The main tectonic and thermal events since the end of the Triassic are the Late Jurassic–Early Cretaceous (Early Alpine) and Late Cretaceous–Paleogene (Late Alpine) compression separated by Late Cretaceous volcanic-arc magmatism and intra/back-arc extension and basin formation. During most of the Cenozoic, the area was mainly under post-orogenic extension. Here, we present the first apatite and zircon fission-track results and new muscovite and biotite ⁴⁰Ar/³⁹Ar analysis on upper Carboniferous–Permian granitoids together with Upper Cretaceous volcanic and subvolcanic rocks and Upper Maastrichtian–Danian conglomerates from the Panagyurishte basin, which allowed us to reveal the Alpine thermal and tectonic evolution of the central parts of the Sredna Gora Zone. Our new results disclosed the existence of several thermal and cooling episodes related to different tectonic and magmatic events in the studied area. The ⁴⁰Ar/³⁹Ar dating of samples from the metamorphic basement constrain the thermal peak of an Early Alpine thermal event at about 140–138 Ma at temperatures between ~ 300 and 400 °C. Through the apatite FT dating and thermal modelling, the time of a Late Alpine (post-Danian) event was constrained at 65–55 Ma, during which the tectonically buried sediments of the Panagyurishte basin reached temperatures of <120 °C. The post-early Eocene cooling and exhumation of the central parts of the Sredna Gora Zone metamorphic basement was related to post-orogenic extension and denudation which took place probably in two stages during the middle Eocene to Oligocene.