A better understanding of the expected future cyclonic activity, especially in the Mediterranean Basin in winter, is essential for developing scientifically based adaptation and mitigation methods to extreme precipitation and wind anomalies. The aim of this study is to analyze the change of winter cyclonic activity in the Mediterranean-Black Sea region, within the Atlantic–European region, at the beginning (as the recent historical period), middle and end of the 21st century. The projections are based on an ensemble of seven CMIP6 models, which showed the best consistency with NCEP/NCAR and ERA5 reanalysis, under the intermediate SSP2-4.5 and highest-emission SSP5-8.5 scenarios. The results show a consistent increase of the frequency of cyclones over Central Europe and the British Isles associated with the shift of cyclone tracks: norward from the Western Mediterranean region and southward from the Iceland Low. The latter leads to a decrease of the frequency in the north of the Atlantic–European region. At the same time, there is a reduction of the frequency of cyclones over the east of the Mediterranean Sea consistent with the decrease of cyclogenesis events. Area-averaged cyclone numbers in the Western and Eastern Mediterranean and the Black Sea subregions reduce to the end of the century under the highest-emission scenario, but not constantly and with a raise in the middle of the 21st century under both scenarios, which may be linked to the long-term multidecadal variability or regional features. In general, our study shows that the future winter cyclonic activity in the Mediterranean-Black Sea region responds unevenly to global climate changes, because regional and monthly features are important, as well as accounting for the long-term quasiperiodic variability.