FCI Tallinn won their first title after defeating Tammeka 2–0 in the final.
The winner of the Cup were to qualify for the 2017–18 UEFA Europa League, but as FCI Tallinn were already qualified for the Champions League as 2016 Meistriliiga champions the spot passed to Flora.
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.
[1] These teams were not drawn and secured a place in the second round without playing: The draw for the second round was made on 16 June 2016.
[4] The draw for the fourth round was made on 21 September 2016.