Cholinesterase (ChE) inhibitors are commonly approved for the Alzheimer’s disease therapy which should restore the original levels of acetylcholine in the brain. In this work, a suitable purification procedure of ChE inhibitors from wild strawberry (Fragaria vesca L.) and apricot (Prunus armeniaca L.) fruit is presented. Activity-guided purification was based on ultrafiltration (0.2 μm → 5 kDa → 3 kDa) of water extract from fruit followed by preparative chromatography (Sephadex LH-20 and HPLC-C18) and analytical HPLC-C18. At every stage of purification, anti-ChE activity was measured in each fraction using Ellman’s colorimetric method. The most active ChE inhibitor purified from both fruits was quercetin and the chemical structure was confirmed by infrared (IR) and proton nuclear magnetic resonance (1H-NMR) spectroscopies. The fast purification procedure can be used for isolating phenolic ChE inhibitors from other fruits from the Rosaceae family.