In this study, the JIP test was used to assess the drought tolerance of two sweet cherry cultivars (Prunus avium L.) (modern and autochthonous). Plants were exposed to progressive drought by withholding water and their fast (< 1 s) chlorophyll fluorescence kinetics was evaluated. JIP test analysis showed that drought stress caused a greater decrease in performance indices (PIABS and PItotal) in a modern cultivar, as compared to an autochthonous one. Our results suggest that limited reoxidation of primary quinone electron acceptor (QA), higher amount of secondary quinone electron acceptor (QB-) nonreducing reaction centres, or inhibition of the electron transport between QA and QB, decreased more seriously the photosynthetic performance of the modern cultivar. Further, higher positive L- and K-bands observed for the modern cultivar also suggest lower energetic connectivity between PSII units and increased inhibition of oxygen-evolving complex over autochthonous cultivar. Our results suggest that the autochthonous cultivar Crveni hrušt had better photosynthetic performance under drought conditions, compared to the modern cultivar New Star.