The AFC Competitions Committee proposed a revamp of the AFC club competitions on 25 January 2014, which was ratified by the AFC Executive Committee on 16 April 2014. The 46 AFC member associations (excluding the associate member Northern Mariana Islands) are ranked based on their national team's and clubs' performance over the last four years in AFC competitions, with the allocation of slots for the 2015 and 2016 editions of the AFC club competitions determined by the 2014 rankings:
The associations are split into West Zone and East Zone, with 23 associations in each zone:
East Zone consists of the associations from ASEAN and East Asia, plus India and Maldives
In each zone, there are a total of 12 direct slots in the group stage, with the 4 remaining slots filled through play-offs.
The top 12 associations in each zone as per the AFC rankings are eligible to enter the AFC Champions League, as long as they fulfill the AFC Champions League criteria.
The top six associations in each zone get at least one direct slot in the group stage, while the remaining associations get only play-off slots:
The associations ranked 1st and 2nd each get three direct slots and one play-off slot (in play-off round).
The associations ranked 3rd and 4th each get two direct slots and two play-off slots (one in play-off round, one in preliminary round 2).
The associations ranked 5th each get one direct slot and two play-off slots (both in preliminary round 2).
The associations ranked 6th each get one direct slot and one play-off slot (in preliminary round 2).
The associations ranked 7th to 12th each get one play-off slot (in preliminary round 1).
The maximum number of slots for each association is one-third of the total number of clubs in the top division (e.g., Australia can only get a maximum of three total slots as there are only nine Australia-based clubs in the A-League).
The AFC Competitions Committee finalised the slot allocation for the 2015 and 2016 editions of the AFC Champions League based on the criteria, including the AFC rankings and the implementation of club licensing regulations, on 28 November 2014.
The following table shows the slot allocation for the 2016 AFC Champions League, which are adjusted accordingly since some of the slots are unused.
The following 45 teams from 17 associations entered the competition.
In the following table, the number of appearances and last appearance count only those since the 2002–03 season (including qualifying rounds), when the competition was rebranded as the AFC Champions League.
In the qualifying play-off, each tie was played as a single match. Extra time and penalty shoot-out were used to decide the winner if necessary (Regulations Article 10.2). The eight winners of the play-off round advanced to the group stage to join the 24 direct entrants. All losers in each round which were from associations with only play-off slots entered the AFC Cup group stage.
The bracket of the qualifying play-off was determined by the AFC based on the association ranking of each team, with the team from the higher-ranked association hosting each match. Teams from the same association could not be placed in the same play-off.
The draw for the group stage was held on 10 December 2015, 16:00 MYT (UTC+8), at the Petaling Jaya Hilton Hotel in Kuala Lumpur, Malaysia. The 32 teams were drawn into eight groups of four. Teams from the same association could not be drawn into the same group.
In the group stage, each group was played on a home-and-away round-robin basis. The winners and runners-up of each group advanced to the round of 16.
The teams were ranked according to points (3 points for a win, 1 point for a draw, 0 points for a loss). If tied on points, tiebreakers would be applied in the following order (Regulations Article 11.5):
Greater number of points obtained in the group matches between the teams concerned;
Goal difference resulting from the group matches between the teams concerned;
Greater number of goals scored in the group matches between the teams concerned;
Greater number of away goals scored in the group matches between the teams concerned;
If, after applying criteria 1 to 4, teams still have an equal ranking, criteria 1 to 4 are reapplied exclusively to the matches between the teams in question to determine their final rankings. If this procedure does not lead to a decision, criteria 6 to 10 apply;
Goal difference in all the group matches;
Greater number of goals scored in all the group matches;
Penalty shoot-out if only two teams are involved and they are both on the field of play;
Fewer score calculated according to the number of yellow and red cards received in the group matches (1 point for a single yellow card, 3 points for a red card as a consequence of two yellow cards, 3 points for a direct red card, 4 points for a yellow card followed by a direct red card);
Team who belongs to the member association with the higher AFC ranking.
In the quarter-finals, the four teams from the West Zone were drawn into two ties, and the four teams from the East Zone were drawn into the other two ties, with the order of legs also decided by the draw.
The draw for the quarter-finals was held on 9 June 2016, 16:00 MYT (UTC+8), at the Petaling Jaya Hilton Hotel in Kuala Lumpur, Malaysia. There was no seeding or country protection, so teams from the same association could be drawn into the same tie.
^The El Jaish v Al-Nasr first leg, originally won 3–0 by Al-Nasr, was forfeited and awarded 3–0 to El Jaish by the AFC Disciplinary Committee on 12 September 2016, as Al-Nasr fielded the player Wanderley who was found to be registered using a fake Indonesian passport.
In the semi-finals, the two quarter-final winners from the West Zone play each other, and the two quarter-final winners from the East Zone play each other, with the order of legs determined by the quarter-final draw.
In the final, the two semi-final winners play each other, with the order of legs reversed from the previous season's final, with the team from the East Zone hosting the first leg, and the team from the West Zone hosting the second leg.
On 25 January 2016, the AFC announced changes to the group stage schedule due to Saudi Arabia's refusal to play in Iran. After the changes, all matches between teams from Iran and Saudi Arabia (including possible play-off winners) were rescheduled to be played on matchdays 5 and 6 (19–20 April and 3–4 May). The venues of these matches would be decided after an evaluation deadline of 15 March 2016. As there had not been a return to normal relations between the two countries by then with Saudi Arabia refusing to lift their travel restrictions to Iran, the AFC accepted the Saudi Arabian Football Federation's proposal of playing all matches between teams from Iran and Saudi Arabia in neutral venues. The Saudi Arabian Football Federation supports its clubs who refuse to travel to Iran. The Iranian Football Federation has stated that it could withdraw from the AFC Champions League due to the venue changes.