The Vertiskos Unit of northern Greece is an elongated basement belt with a complex poly-metamorphic history. It extends from Greece (Chalkidiki peninsula), to the south, up to Serbia, in the north, and arguably represents the westernmost part of the Rhodope Metamorphic Province (northern Greece to southern Bulgaria). The Vertiskos Unit experienced a medium pressure lower amphibolite-facies metamorphic overprint during the Alpine Orogeny. The available medium-temperature geochronology implies that it remained at temperature of approximately 300°C (or slightly higher) during Lower Cretaceous. In order to constrain its post-Lower Cretaceous thermal history, until near-surface exposure, we applied apatite fission track analysis. The central ages obtained range from 68.5 ± 3.8 to 46.6 ± 3.6 Ma (uppermost Cretaceous to Middle Eocene) and mean track lengths between 13 and 13.5 μm. We applied two inverse thermal modeling approaches using either each sample independently (high degree of freedom in the thermal history, better data fit) or all samples together interpreting them as a vertical profile (simpler thermal history, worse data fit). Irrespective of the modeling approach, we conclude that the bulk thermal history of the Vertiskos Unit crosses the high-temperature limit of the apatite partial annealing zone by the uppermost Cretaceous and reaches near-surface conditions as early as lower/middle Eocene. These results contrast with the thermal history of the other domains of the Rhodope Metamorphic Province further east (namely the Southern Rhodope Core Complex and the Northern Rhodope Complex) and establish the Vertiskos basement complex as the oldest exhumed coherent basement fragment of the Rhodope Metamorphic Province and Greece.