Bilberry fruit is a valuable source of many antioxidant and anticholinesterase agents. Thus, the aim of the present study was to determine the effect of heat treatment combined with enzyme preparations on the antioxidant and anticholinesterase activity of bilberry juices. Each bilberry juice efficiently ‘scavenged’ DPPH and ABTS radicals. The highest ability to remove DPPH radicals was found in pre-heated (80–90°C, 5 min) and non-heated (only 50–55°C, 2 h) juices obtained using Pectinex BE XXL. The pre-heating treatment caused an increase in the anti-acetylcholinesterase activity compared to non-heated juices, with the highest elevation (p < 0.05) recorded for juice produced using Panzym BE XXL. Similarly, the heat pretreatment caused an increase in the anti-butyrylcholinesterase activity in bilberry juices. The combined application of pre-heating and enzyme preparations during juice processing resulted in an increase in the antioxidant and anticholinesterase activities of the end juices.