The competition started on 20 August 2016 with the first preliminary round and concluded with the final at the Zimbru Stadium on 25 May 2017.

All ties level after 90 minutes used extra time to determine the winner, with a penalty shoot-out to follow if necessary.

[3] Number in brackets denote the level of respective league in Football in Moldova 28 clubs from the Divizia B entered this round.

Teams that finished higher on the league in the previous season played their ties away.

Teams that finished higher on the league in the previous season played their ties away.

Teams in bold continue to the next round of the competition.Rîșcani, Intersport Sănătăuca, Maiac Cioropcani, Grănicerul Glodeni, Cruiz Camenca, Sinteza Căușeni, Anina Anenii Noi, Sparta Chișinău, Sireți and Congaz received a bye for the second preliminary round.

The home teams and the pairs for 3 Divizia Națională sides were determined in a draw held on 7 September 2016.

The 7 winners from the previous round and Gagauziya-Oguzsport joined the remaining 8 Divizia Națională sides seeded 1-8.