A newly acquired CounterCurrent Supercritical Fluid Fractionation (CC-SFF) packed column was putted into operation by studying the separation of key apple aroma constituents from aqueous solutions using supercritical carbon dioxide (CO2). This work studied the effect of temperature (40–60°C), pressure (8–14MPa) and solvent-to-feed ratio (S/F) (5–15kgkg−1 CO2/feed) on the fractionation and concentration of characteristic six-carbon (C-6) apple aromas ((E)-2-hexenal and hexanal) from less important compounds such as 1-hexanol and water. At the selected temperatures and pressures CO2 densities were in the range of 192–763kgm−3. Very high separation factors from water were observed (∼104). Two separate phases were obtained in the extract, demonstrating that CC-SFF of aqueous apple aromas is highly capable of producing a water-free super-concentrated product. However, little fractionation of aromas from less important compounds such 1-hexanol was achieved. The highest concentration of C-6 apple aromas in the total extract was approx. 20% w/w, and the extraction yield of aromas was >86%. Response Surface Methodology (RSM) with a Box-Behnken design was used to investigate and optimize the process variables. Significant surface models (P-values<0.0001) for the total yield of extraction and the organics’ loading showed that the S/F had the most significant effect on the extraction of C-6 apple aroma compounds. Additionally, according to the RSM models 40°C, 14MPa, and S/F=5 to would be optimum condition to concentrate C-6 apple aromas.