Climate change is inherently linked to long-term non-stationary changes in the characteristics and frequency of weather patterns. The present study attempts to identify the statistical changes of weather patterns in Athens Greece, from the comparative assessment of 96-h backward trajectories between historic (1980–2009) and future (2020–2049) climatology derived from the IPCC RCP4.5 and RCP8.5 scenarios. Arrival heights at 750 m, 1500 m, and 3000 m above sea level are considered to account for the impact of the planetary boundary layer and the lower free troposphere. The analysis of the historic period yields 7 dominant patterns for all heights determined independently, with similar spatial characteristics but varying frequency of occurrence. The classification of backward trajectories under future climate using the same historic clusters reveals percentage changes from locally short-distance travelling patterns to longer-distance ones with a predominant northbound direction. As a second experiment, backward trajectories are re-clustered independently reaching again the same type of clusters but with observable changes in the cluster origins and trajectory lengths.