Bengaluru FC were the reigning champions of the Federation Cup, having won the tournament in 2015.

All matches except the final were played as two-legged tie on home and away basis, with the application of the away goals rule.

The final was played as a single match at the Indira Gandhi Stadium in Guwahati.

[2] Mohun Bagan defeated Aizawl 5–0 to clinch their record 14th title, making them the most successful club in the history of the competition.

[3] In 2015, All India Football Federation decided to scrap Federation Cup due to congested calendar with I-League and Indian Super League occupying a large part of the calendar, but after Asian Football Confederation mandated that a club must play 18 matches in the season, AIFF decided to revive the tournament.