The 2016–17 Estonian Cup is the 27th season of the Estonian main domestic football knockout tournament. The winner of the Cup will qualify for the first qualifying round of the 2017–18 UEFA Europa League. The tournament began in May 2016, and the final will take place in May 2017 at the A. Le Coq Arena. Flora Tallinn are the current cup holders.
The draw was made by Estonian Football Association on 21 May 2016, on the half-time of the 2015–16 final of the same competition.
League level of the club in the brackets.
Rahvaliiga RL (people's league) is a league organized by Estonian Football Association, but not part of the main league system.
Notes
Note 1: Tallinna JK Ararat TTÜ withdrew from the competition.
Note 2: SK Roosu withdrew from the competition.
Note 3: JK Pedajamäe withdrew from the competition.
Note 4: JK Kaitseliit Kalev dissolved before the competition.
Note 5: JK Väätsa Vald withdrew from the competition.
These teams were not drawn and secured a place in the second round without playing:
Meistriliiga (Level 1): Tallinna FC Infonet, JK Narva Trans, Paide Linnameeskond, Tallinna FC Levadia,
Esiliiga (2): FC Flora U21
Esiliiga B (3): Raasiku FC Joker, Viimsi JK
II Liiga (4): Jõgeva SK Noorus-96, Saue JK Laagri, Jõhvi FC Lokomotiv, Türi Ganvix JK, FC Kose, Viimsi JK II, Kiviõli FC Irbis, Tõrva JK, Tallinna JK Legion,
III Liiga (5): EMÜ SK, Tartu Ülikool Fauna, FC Tartu, SK Imavere Forss, Maardu United, JK Loo, Läänemaa JK Haapsalu, Nõmme Kalju FC III
IV Liiga (6): Tallinna JK Jalgpallihaigla, Tallinna Jalgpalliselts, Rumori Calcio Tallinn
The draw for the second round was made on 16 June 2016.
Notes
Note 6: EMÜ SK were awarded a win as Castovanni Eagles fielded an unregistered player. The original score was 9–1.
Note 7: Molycorp Silmet were awarded a win as SK Imavere Forss fielded an unregistered player. The original score was 2–3.
The draw for the third round was made on 11 August 2016.
The draw for the fourth round was made on 21 September 2016.
The draw was made on 28 February 2017.
