The 2016–17 EMUFA Cup was the fifth edition of the EMUFA Cup, which began on 31 August 2016 with the first qualifying round and culminated with the final in May 2017. Forty-one teams participated in the competition from twenty-two nations.
List of qualified teams
Qualifying stages
First qualifying round
The first qualifiers were held over two legs, with the first leg being played on 31 August 2016, and the second on 7 September 2016. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
Second qualifying round
The second qualifiers were held over two legs, with the first leg being played on 14 September 2016, and the second on 21 September 2016. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
Third qualifying round
The third qualifiers were held over two legs, with the first leg being played on 28 September 2016, and the second on 5 October 2016. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
Group stage
Group A
Group B
Group C
Group D
Group E
Group F
Knock-out stages
Round of 16
The second round was held over two legs, with the first leg being played on 11 January 2017, and the second on 18 January 2017. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
Mercury City win 3–2 on aggregate.
May Wanderers win 2–1 on aggregate.
Hanseong AFC win 2–1 on aggregate.
West Grinstead FC win 3–1 on aggregate.
Concordia Kronau win 4–3 on aggregate.
Scores tied at 2–2 on aggregate. Ad & Tkir United win on away goals.
Harbourside Football win 2–0 on aggregate.
Kilbay Rangers win 3–1 on aggregate.
Quarter-finals
The quarter-finals were held over two legs, with the first leg being played on 15 February 2017, and the second on 1 March 2017. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
West Grinstead FC win 4–1 on aggregate.
Mercury City win 3–0 on aggregate.
May Wanderers win 3–0 on aggregate.
Ad & Tkir United win 3–2 on aggregate.
Semi-finals
The semi-finals were held over two legs, with the first leg being played on 29 March 2017, and the second on 12 April 2017. Ties were settled by the away goals rule after 90 minutes, or by extra time and penalties if there was still no winner.
Mercury City win 4–2 on aggregate.
Ad & Tkir United win 2–0 on aggregate.
Final
The final was held over a single match, held on 24 May 2017. If the match were drawn, extra time and penalties were to be used to settle the tie.