The influence of operating temperature on membrane permeability was studied and compared with the effect of temperature on the driving force for permeation. A hydrophobic polyoctylmethyl siloxane membrane was used. For the feed mixture, an aqueous solution of aroma compounds containing four alcohols, one aldehyde, and five esters, all of which are important contributors to apple juice flavor, was used. Temperature had a strong effect on mass transfer and selectivity, both of which increased with increasing temperature. However, the selectivity for a component with a high activation energy for permeation increased more with temperature than did a component with a low activation energy for permeation. This caused a variation in the aroma composition of the permeate. The study showed that it is possible to estimate the activation energy for permeation of aroma compounds, and thus the influence of temperature on the internal mass transfer, through their hydrophobicity, size, and a complementary comparison of the activation energies for permeation for some other permeants of the same chemical group.