The flavonoid rutin presents several pharmacological effects, despite this, its application in the pharmaceutical industry can be significantly limited by its low bioavailability. The development of lipophilic derivatives by esterification of hydroxyl groups with fatty acid chains may be an effective strategy to change their physicochemical properties. This work aims to use high-speed countercurrent chromatography (HSCCC) to isolate rutin esters produced by esterification reactions catalyzed by the immobilized lipase from Candida antarctica (Novozyme 435®). The lipase-catalyzed synthesis of rutin esters (R3-R18:2) in 2-methyl-2-butanol exhibited conversions that ranged from 16 to 40% and highest conversion for short chain fatty acids (R4-R12). After initial partitioning tests of the reaction mixture in different solvent proportions followed by thin layer chromatography (TLC) analysis, the biphasic solvent systems consisting in HEMWat (hexane/ethyl acetate/methanol/water) in different proportions were chosen to separate rutin esters. These esters were separated for the first time to the reaction mixture via HSCCC. This technique proved to be more advantageous than the traditionally one since it allowed quick isolation and high purity (≥ 90%) of the products. It also permitted a substrate recovery for reuse in other enzymatic reactions. Furthermore, the results add valuable information, specially concerning the structures elucidation of different rutin esters not previously described.