The 2016 Kyrgyzstan Cup was the 25th season of the Kyrgyzstan Cup knockout tournament. The cup winner qualified for the 2017 AFC Cup.
Ala-Too 0-3 Abdish-Ata-2 Alay 2-1 Abdish-Ata Alga 2-4 Dordoy Aldier 1-1 Alay-2
First Legs Alay-2 0-6 Alay Dordoy 5-0 Abdish-Ata-2 Second Legs Alay 4-0 Alay-2 Abdish-Ata-2 2-3 Dordoy
Dordoy 1-0 Alay